App window(s) kind of frozen and partially unresponsive to mouse input?

After many years struggling with sluggish slow gtk4 (vs gtk3) and nothing helped, no fallback render, etc. (see my older posts), even on a very capable but about 10 years old GPU (Nvidia GTX 1070) on a i9 and i7 system. Simply a file chooser goes to a crawl… Now I upgraded to a modern AMD GPU Radeon RX9070 on the i9 (Gnome 48, Debian stable/Trixie 13) and RX9060 XT on the i7 machine (see details below). So that help general performance big time and gtk4 got super snappy – as a fact finding it sadly requires modern GPU hardware to be usable.

Fine.

With Debian Testing I now got forced to Wayland/Gnome (V50).

But I am running into a new very odd issue I was reading up on a though it was fixed with version 50, but obviously not.

My app is working initially, but once I open a few more windows at random I looses “mouse” control to them. I can move/resize them only using keyboard Option+Mouse/Mouse MMB. And most functions/button menus suddenly stop been functional also.

Google AI dug out this, I do not know much about it yet, but this about aligns with what I see.
Only I see it also on Gnome 50.

Any thoughts, hints, fixes?


The i7 system details:

System Details Report


Report details

  • Date generated: 2026-06-14 20:50:36

Hardware Information:

  • Hardware Model: Gigabyte Technology Co., Ltd. Z170X-Gaming 7
  • Memory: 32.0 GiB
  • Processor: Intel® Core™ i7-6700K × 8
  • Graphics: AMD Radeon™ RX 9060 XT
  • Disk Capacity: 16.5 TB

Software Information:

  • Firmware Version: F22m
  • OS Name: Debian GNU/Linux forky/sid
  • OS Build: (null)
  • OS Type: 64-bit
  • GNOME Version: 50
  • Windowing System: Wayland
  • Kernel Version: Linux 6.12.85+deb13-amd64

Update:
I think I found the culprit as a side effect:

I had a brief notification/progress info shown in a popover and I closed it via popdown.
I did not liked it grabbing focus so I added this

gtk_popover_set_autohide(GTK_POPOVER(popover), FALSE);

and for odd reasons this solved all the issues?!?! Still do not understand this but works now!