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Win10, TVP 11.7.1 STD
For some reason the FX window becomes of the same color as a selected layer. It is gone temporarily when I open the Preferences window, but then it's manifesting again when I minimize the FX or when I undo/redo while FX panel is open,
see screenshot

Hello Soom, from what I see on my computer, the latest FX you have selected/modified/uncollapsed stays highlighted. You are visibly using custom TVPaint interface colors, a screenshot of your color scheme list from the preferences would help me identify which modified interface color might cause this.
A short video of the issue would help a lot, I have just tested this on 11.5.3 and the behavior seems to be the same, but I might have missed something.

Hi Dean
I have checked it at home on my mac, and - uh oh! You are right - I have just realized that it was like this all the time, but because I was using darker colors at home, I never paid attention to this. The "Backround Current" color is the same for the selected layer and for the selected FX. The problem with that is that I sometimes use brighter colors for selected layers, but I don't need it on the FX, because then I barely see the elements there.
Here is a screenshot - you can see my Background Color is now set to white, and it's the same white in the FX, although it's always off when Preferences panel is open, so you don't see it now. And here is a video recording:

I see, maybe those 2 colors could be separated in a future version but not in the shorter term.