Hello,

In tr 1 gog version, if you start the game, go to croft manor, then close the game. Any full screen window overlaps the taskbar. I.e. No taskbar unless you minimise or close all Windows. There are two fixes. Restart the game and close it or restart the pc.

Does anyone know how to prevent it in the first place? I fear gogs tweaks are the root cause but I don't know what to change

There's no easy solution, but some workarounds exist.  Take a look at <span class="bold">this thread</span>.  ;-)