I get the same EPERM message, but my Thunderbird is running fine. (That said, I don’t use Gmail.)
So possibly your actual problem is unrelated to any of the terminal output 
Hi Steve,
I did revert the changes but this doesn’t make any difference.
As I also answered I did Thunderbird rollbacks but nothing works.
One thing I did not yet write here is this:
When I try to get e-mails, and I know there are e-mails on the server waiting, I get this:
Could not connect to server pop.gmail.com; the connection was refused.
I checked and double-checked log-in name and password a couple of times, copied them from a safe source, but still I get this.
I have some more info which I hope might help:
flatpak run --verbose org.mozilla.Thunderbird
F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/jan/.local/share/flatpak
F: Opening user flatpak installation at path /home/jan/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: Skipping parental controls check for app/org.mozilla.Thunderbird/x86_64/stable since parental controls are disabled globally
F: Opening user flatpak installation at path /home/jan/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: /var/lib/flatpak/runtime/org.freedesktop.Platform/x86_64/24.08/5365bb0e377aa4dc0ebb3ddbc5af846eb1cfa9222146754997d615b6c8c63f0b/files/lib32 does not exist
F: Cleaning up unused container id 3186093621
F: Cleaning up per-app-ID state for org.mozilla.Thunderbird
F: Allocated instance id 2585915660
F: Add defaults in dir /org/mozilla/Thunderbird/
F: Add locks in dir /org/mozilla/Thunderbird/
F: Not sharing "/home/jan/.gnupg" with sandbox: Unable to open path "/home/jan/.gnupg": No such file or directory
F: Allowing wayland access
F: Allowing pulseaudio access
F: Pulseaudio user configuration file '/home/jan/.config/pulse/client.conf': Error opening file /home/jan/.config/pulse/client.conf: No such file or directory
F: CUPS configuration file '/home/jan/.cups/client.conf': Error opening file /home/jan/.cups/client.conf: No such file or directory
F: Running '/usr/bin/bwrap --args 43 -- /usr/bin/xdg-dbus-proxy --args=42'
F: Running '/usr/bin/bwrap --args 41 -- thunderbird'
[2] Sandbox: CanCreateUserNamespace() clone() failure: EPERM
[2, Main Thread] WARNING: Locale not supported by C library.
Using the fallback 'C' locale.: 'glib warning', file /builds/worker/checkouts/gecko/toolkit/xre/nsSigHandlers.cpp:201
(thunderbird-esr:2): Gtk-WARNING **: 15:03:32.838: Locale not supported by C library.
Using the fallback 'C' locale.
[Parent 2, Main Thread] WARNING: Running in confined mode, using Portal notifications. Some features and hints won't be supported: 'glib warning', file /builds/worker/checkouts/gecko/toolkit/xre/nsSigHandlers.cpp:201
(org.mozilla.Thunderbird:2): libnotify-WARNING **: 15:03:34.184: Running in confined mode, using Portal notifications. Some features and hints won't be supported
Can you see what:
flatpak config
returns
You may need to set your locale in flatpak as well.
flatpak config --set languages 'en;nl'
flatpak update
pop.gmail.com requires the following config:
pop.gmail.com
Requires SSL: Yes
Port: 995
You have SSL turned on and you’re banging on port 995?
Hi Joe, tis is what I get:
flatpak config
languages: *unset* (default: en)
extra-languages: *unset*
Isn’t that a bit strange? I mean, I have never had to do that, so why now? I can try it of course and see what happens. Did you also do this?
flatpak config --set languages 'en;nl'
flatpak update
Looking for updates…
ID Branch Op Remote Download
1. [✓] com.rawtherapee.RawTherapee.Locale stable u flathub 1,0 kB / 20,3 kB
2. [✓] org.darktable.Darktable.Locale stable u flathub 257,4 kB / 9,0 MB
3. [✓] org.freedesktop.Platform.Locale 24.08 u flathub 1,9 MB / 388,2 MB
4. [✓] org.freedesktop.Platform.Locale 25.08 u flathub 648,5 kB / 378,2 MB
5. [✓] org.gnome.Platform.Locale 48 u flathub 100,2 kB / 394,8 MB
6. [✓] org.gnome.Platform.Locale 49 u flathub 24,6 kB / 384,9 MB
7. [✓] org.inkscape.Inkscape.Locale stable u flathub 350,3 kB / 14,4 MB
8. [✓] org.kde.Platform.Locale 5.15-24.08 u flathub 327,8 kB / 409,6 MB
9. [✓] org.kde.Platform.Locale 5.15-25.08 u flathub 10,2 kB / 400,0 MB
10. [✓] org.kde.Platform.Locale 6.8 u flathub 284,0 kB / 409,4 MB
11. [✓] org.kde.Platform.Locale 6.9 u flathub 134,6 kB / 409,7 MB
12. [✓] org.kde.digikam.Locale stable u flathub 1,5 MB / 113,1 MB
13. [✓] org.kde.elisa.Locale stable u flathub 233,0 kB / 14,7 MB
14. [✓] org.kde.kate.Locale stable u flathub 117,2 kB / 5,7 MB
15. [✓] org.kde.kdenlive.Locale stable u flathub 212,0 kB / 5,6 MB
16. [✓] org.kde.krita.Locale stable u flathub 310,5 kB / 12,7 MB
17. [✓] org.kde.ktorrent.Locale stable u flathub 53,2 kB / 2,5 MB
18. [✓] org.libreoffice.LibreOffice.Locale stable u flathub 1,1 MB / 89,3 MB
19. [✓] org.mozilla.Thunderbird.Locale stable u flathub 420,5 kB / 5,5 MB
20. [✓] org.mozilla.firefox.Locale stable u flathub 390,9 kB / 36,8 MB
Updates complete.
I then rebooted and started Thunderbird from the terminal again but nothing changes:
flatpak run --verbose org.mozilla.Thunderbird
F: No installations directory in /etc/flatpak/installations.d. Skipping
F: Opening system flatpak installation at path /var/lib/flatpak
F: Opening user flatpak installation at path /home/jan/.local/share/flatpak
F: Opening user flatpak installation at path /home/jan/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: Skipping parental controls check for app/org.mozilla.Thunderbird/x86_64/stable since parental controls are disabled globally
F: Opening user flatpak installation at path /home/jan/.local/share/flatpak
F: Opening system flatpak installation at path /var/lib/flatpak
F: /var/lib/flatpak/runtime/org.freedesktop.Platform/x86_64/24.08/5365bb0e377aa4dc0ebb3ddbc5af846eb1cfa9222146754997d615b6c8c63f0b/files/lib32 does not exist
F: Allocated instance id 1873946344
F: Add defaults in dir /org/mozilla/Thunderbird/
F: Add locks in dir /org/mozilla/Thunderbird/
F: Not sharing "/home/jan/.gnupg" with sandbox: Unable to open path "/home/jan/.gnupg": No such file or directory
F: Allowing wayland access
F: Allowing pulseaudio access
F: Pulseaudio user configuration file '/home/jan/.config/pulse/client.conf': Error opening file /home/jan/.config/pulse/client.conf: No such file or directory
F: CUPS configuration file '/home/jan/.cups/client.conf': Error opening file /home/jan/.cups/client.conf: No such file or directory
F: Running '/usr/bin/bwrap --args 43 -- /usr/bin/xdg-dbus-proxy --args=39'
F: Running '/usr/bin/bwrap --args 41 -- thunderbird'
[2] Sandbox: CanCreateUserNamespace() clone() failure: EPERM
Yes, I do. It is not an account which I just added to Thunderbird, it is one which goed back many years and it has always worked. So, I don’t understand why not now. What happend, what is different?
Thank you all for spending your time on me, it is greatly appreciated.
You’re going to force me to install Thunderbird now, so I can replicate it!
Bedankt! 
I never said that and you know it. 
I was thinking is it an error at the Gmail side, because of this error Thunderbird gives when I try to get my mail from the server:
Could not connect to server pop.gmail.com; the connection was refused.
When I open my mail on the Gmail website and I use the exact same credentials it works, no problems then so I guess it is not Gmail.
Bedankt Steve. 
Apparently I’ve had thunderbird on here before (no idea when) but I had config lying around as it defaults to this:
Can you tell me (as I have no idea) how to change Thunderbird from IMAP over to pop3? I can confirm that imap using that server works ok, but until I determine how to switch to pop based email collection, I’m a bit stuck.
On the other hand, I installed Tbird from rpm (vanilla sudo dnf install thunrderbird) and the only logging messages I get on the console are as follows, from 2 invocations and a bit of fiddling with the config inside Thunderbird
┌─🎩 lurcher ~
├─
└─➜ thunderbird ⏱️ 28s 14:46 Mon 24-Nov
[28903] Sandbox: seccomp sandbox violation: pid 28903, tid 28903, syscall 16, args 2 2150388778 140736466130928 18446744073709551608 139694286337056 0.
┌─🎩 lurcher ~
├─
└─➜ [29469] Sandbox: seccomp sandbox violation: pid 29469, tid 29469, syscall 16, args 2 2150388778 140720772008416 18446744073709551608 140601552491552 0. ⏱️ 1m29s 14:47 Mon 24-Nov
[29988] Sandbox: seccomp sandbox violation: pid 29988, tid 29988, syscall 16, args 2 2150388778 140725922582672 18446744073709551608 140219726763040 0.
[30125] Sandbox: seccomp sandbox violation: pid 30125, tid 30125, syscall 16, args 2 2150388778 140725579401696 18446744073709551608 140572939564064 0.
I see you have something wrong in your screenshot:
@ Server Name it says smtp.gmail.com on Port 993. The Imap server @ Gmail is named imap.gmail.com.
SMTP is for sending mail.
If you can’t change the data here to pop.gmail.com on port 995 then adding a new account is probably the only way to do it.
You’re quite correct - I changed it to pop to test, found I could not connect on 994 as I’m configured to use imap and changed the port back to 993 and retyped the server name by hand… whilst reading the “Outgoing Mail (SMTP)” at the end of that panel on the left and muscle memory typed it by itself.
Good spot - I’d likely never have noticed that as I don’t use Tbird at all!
Been there, done that.
It’s magic.
I was just checking a route on Google maps when I received a notification that all the mails which were waiting on the server were received by Thunderbird. I checked Thunderbird and yes, there they are. I have no idea what happened.
Will do some tests now.
Yes, I can receive mails coming from another email-address I have and I can also answer that one. It seems it works again.
No, I haven’t done anything related to this problem in the mean time. No idea what happened.
Was something wrong at Gmail after all?
I will keep monitoring it, but in the mean time Thank you all for your time, knowledge and spirit to help me. It’s always amazing when something like this happens.