Windows disappear for several applications at once, but not all

After doing a software update with the software gui this morning, I get incidents, randomly, on the timescale of about an hour where several of my windows disappear, all at once, but not all of them. Running Gnome Shell with Wayland. The disappearers are xload, xterm, thunderbird, slack, teams, and zoom. The persisters are firefox and gnome-terminal. Of course these lists may not be exhaustive. Have others seen behavior like this?

Wayland is still in development, but mostly stable.
Wayland does have issues with some apps.
Wayland does have issues with some GPUs, notably nvidia, and the drivers in use. The nvidia driver has some issues and the nouveau default driver has some different issues.

For a guess as to the cause we need more info related to hardware, OS, etc.
Which version of fedora?
Is it fully updated?
Please post the output of inxi -Fzxx as preformatted text using the </> tags above and we can start from there. You may need to install inxi.

Fedora 35. The system was fully updated this morning.

  Kernel: 5.16.12-200.fc35.x86_64 x86_64 bits: 64 compiler: gcc
    v: 2.37-10.fc35 Desktop: GNOME 41.4 tk: GTK 3.24.31 wm: gnome-shell dm: GDM
    Distro: Fedora release 35 (Thirty Five)
  Type: Desktop System: Dell product: XPS 8940 v: N/A
    serial: <superuser required> Chassis: type: 3 serial: <superuser required>
  Mobo: Dell model: 0KV3RP v: A00 serial: <superuser required> UEFI: Dell
    v: 1.0.3 date: 07/29/2020
  Info: 8-core model: Intel Core i7-10700 bits: 64 type: MT MCP
    arch: Comet Lake rev: 5 cache: L1: 512 KiB L2: 2 MiB L3: 16 MiB
  Speed (MHz): avg: 1772 high: 4412 min/max: 800/4800 cores: 1: 4230
    2: 4412 3: 800 4: 800 5: 800 6: 800 7: 800 8: 800 9: 800 10: 800 11: 3495
    12: 3200 13: 2558 14: 1988 15: 1275 16: 800 bogomips: 92796
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
  Device-1: Intel CometLake-S GT2 [UHD Graphics 630] vendor: Dell
    driver: i915 v: kernel bus-ID: 00:02.0 chip-ID: 8086:9bc5
  Device-2: NVIDIA TU106 [GeForce RTX 2060 SUPER] vendor: Dell
    driver: nouveau v: kernel bus-ID: 01:00.0 chip-ID: 10de:1f06
  Device-3: Microsoft LifeCam HD-3000 type: USB
    driver: snd-usb-audio,uvcvideo bus-ID: 1-6:4 chip-ID: 045e:0779
  Display: wayland server: X.Org compositor: gnome-shell driver:
    loaded: modesetting unloaded: fbdev,vesa resolution: 1: 2560x1440~60Hz
    2: 1920x1080~60Hz s-dpi: 96
  OpenGL: renderer: Mesa Intel UHD Graphics 630 (CML GT2)
    v: 4.6 Mesa 21.3.7 direct render: Yes
  Device-1: Intel Comet Lake PCH cAVS vendor: Dell driver: snd_hda_intel
    v: kernel bus-ID: 00:1f.3 chip-ID: 8086:06c8
  Device-2: NVIDIA TU106 High Definition Audio vendor: Dell
    driver: snd_hda_intel v: kernel bus-ID: 01:00.1 chip-ID: 10de:10f9
  Device-3: Microsoft LifeCam HD-3000 type: USB
    driver: snd-usb-audio,uvcvideo bus-ID: 1-6:4 chip-ID: 045e:0779
  Sound Server-1: ALSA v: k5.16.12-200.fc35.x86_64 running: yes
  Sound Server-2: PipeWire v: 0.3.47 running: yes
  Device-1: Realtek vendor: Rivet Networks driver: r8169 v: kernel port: 3000
    bus-ID: 03:00.0 chip-ID: 10ec:2600
  IF: enp3s0 state: up speed: 1000 Mbps duplex: full mac: <filter>
  Device-2: Qualcomm Atheros QCA9377 802.11ac Wireless Network Adapter
    vendor: Dell driver: ath10k_pci v: kernel bus-ID: 04:00.0
    chip-ID: 168c:0042
  IF: wlp4s0 state: down mac: <filter>
  IF-ID-1: virbr0 state: down mac: <filter>
  Device-1: Qualcomm Atheros type: USB driver: btusb v: 0.8 bus-ID: 1-14:11
    chip-ID: 0cf3:e009
  Report: rfkill ID: hci0 rfk-id: 0 state: down bt-service: enabled,running
    rfk-block: hardware: no software: yes address: see --recommends
  Local Storage: total: 4.1 TiB used: 1.99 TiB (48.5%)
  ID-1: /dev/nvme0n1 vendor: SK Hynix model: BC511 NVMe 512GB
    size: 476.94 GiB speed: 31.6 Gb/s lanes: 4 serial: <filter> temp: 43.9 C
  ID-2: /dev/sda vendor: Seagate model: ST2000DM008-2FR102 size: 1.82 TiB
    speed: 6.0 Gb/s serial: <filter>
  ID-3: /dev/sdb type: USB vendor: Samsung model: HD103SI size: 931.51 GiB
    serial: <filter>
  ID-4: /dev/sdc type: USB vendor: Western Digital model: WD10 JPVX-28JC3T1
    size: 931.51 GiB serial: <filter>
  ID-1: / size: 475.35 GiB used: 252.29 GiB (53.1%) fs: btrfs
    dev: /dev/nvme0n1p3
  ID-2: /boot size: 975.9 MiB used: 247.4 MiB (25.3%) fs: ext4
    dev: /dev/nvme0n1p2
  ID-3: /boot/efi size: 598.8 MiB used: 13.8 MiB (2.3%) fs: vfat
    dev: /dev/nvme0n1p1
  ID-4: /home size: 475.35 GiB used: 252.29 GiB (53.1%) fs: btrfs
    dev: /dev/nvme0n1p3
  ID-1: swap-1 type: zram size: 8 GiB used: 1.62 GiB (20.3%) priority: 100
    dev: /dev/zram0
  System Temperatures: cpu: 27.8 C pch: 43.0 C mobo: N/A gpu: nouveau
    temp: 40.0 C
  Fan Speeds (RPM): cpu: 788 fan-2: 1012 gpu: nouveau fan: 1052
  Processes: 641 Uptime: 9h 7m Memory: 31.08 GiB used: 6.42 GiB (20.6%)
  Init: systemd v: 249 runlevel: 5 target: Compilers:
  gcc: 11.2.1 Packages: note: see --pkg flatpak: 17 Shell: Bash v: 5.1.8
  running-in: gnome-terminal inxi: 3.3.12

And another thing that I noticed since posting: running /usr/bin/display to bring up an image file seems to be the culprit more often than not.

I see you do have a dual gpu config with intel UHD 630 and nvidia GeForce RTX 2060. Using the nouveau driver.

Are you using 2 monitors? If so then several have had some issues with wayland and nouveau and the external monitor. I cannot say for sure that the video drivers or the DE is directly related, but they may be. Several have noted issues with zoom, but I do not recall all the details. The fact it affects several other apps at the same time seems to indicate it may be the underlying window manager and not a specific app.

If you are able to identify exactly when the problem occurs then it may be possible to use either dmesg or journalctl to obtain logs for the time involved and see what they tell you. The Xorg log may also have some clues.

Your comment about using /usr/bin/display as possibly related is also something to consider, and that should be easy to test.

Yes. Using two monitors.

Trying to trigger an incident and then looking at the logs is a good idea. Can’t work on that right now, but will give it a try later.

Ran display from the command line. Have not done that recently. Get the following error when the windows disappear:

$ display misc/dealer_button.jpg
X connection to :0 broken (explicit kill or server shutdown).
XIO:  fatal IO error 2 (No such file or directory) on X server ":0"
      after 5650 requests (2551 known processed) with 9 events remaining.

What is the result of file misc/dealer_button.jpg

Have you tried opening that file using the file manager and double clicking on the file name? It should open with the default image viewer in gnome (eye of gnome). The display command is also known as ImageMagic and it works on my jpg files.

Note though that I am using xorg and you are using wayland. It is possible that ImageMagic is not compatible with wayland.

To test that I suggest you log out, then at the login screen select the gear at the lower right corner of the screen and choose to login with gnome and xorg. Then once again do the test with the display command and see if there are different results.

$ file misc/dealer_button.jpg 
misc/dealer_button.jpg: JPEG image data, JFIF standard 1.02, resolution (DPI), density 300x300, segment length 16, Exif Standard: [TIFF image data, big-endian, direntries=7, orientation=upper-left, xresolution=98, yresolution=106, resolutionunit=2, software=Adobe Photoshop CS Windows, datetime=2005:02:01 09:59:03], baseline, precision 8, 250x252, components 1

eog works fine, When I use display, the eog windows persists.

I’ll try Xorg…

No problems seen with Xorg!

That implies the issue is with wayland + ImageMagic. I would suggest you file a bug at Log in to Red Hat Bugzilla to bring the issue to the attention of the developers.