So because of the constant lag of switching between desktops I disabled Animation Effects and it seems to have resolved the icon issue for me. On a side note, disabling the animations is so much nicer as switching desktops is instant now.
Disappearance of Windows 11 Taskbar Icons after Switching Virtual Desktops
Windows 11 22H2
In Windows 11's built-in virtual desktop feature, there is a high probability that icons of active applications on the current desktop may not be displayed when switching between different virtual desktops. The icons only appear when I click on the respective application. I have attempted to resolve the issue through restarts and using Sfc and Dism for repairs, but the problem persists. An essential configuration to note is that the taskbar is set to display windows only from the current desktop.
Windows for home | Windows 11 | Performance and system failures
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172 answers
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Anonymous
2023-12-09T10:26:07+00:00 -
Anonymous
2024-12-18T21:38:00+00:00 Over 13 months since this bug was created, our planet has moved a distance of approximately 643 million miles around the sun, yet Microsoft still haven't found a couple of hours to fix animation issues with virtual desktops.
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Anonymous
2023-12-14T00:44:18+00:00 Pressing Windows+D twice "fixes" this issue. ofcourse the problem might re-emerge but it only takes a second to do this so the issue is non-existent in my mind.
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Anonymous
2023-12-01T13:54:28+00:00 Same version of update (KB5032190), same issue.
It is totally random if or which icons are visible. Reshuffle at every switch of virtual desktops. Sometimes all are there, sometimes even none.However, when clicking on the icon in the taskbar to minimize the window, that specific icon reappears.
I spend a meaningful amount of time, clicking invisible icons on a daily basis...