OK, I made it!
I don’t know why, but two icon files in my light, dark and classic folders in app/Resources were named wrongly. They were named „flowtop_compright.png” and „flowtop_compleft.png” but the program demanded „FlowTop_CompRight.png” and „FlowTop_CompLeft.png” with the capitals! So I’ve changed the names of the files to their proper version and now I can access the preferences menu. Might be a bug, because the FlowBottom icons are named correctly. So that, combined with uninstalling psychtoolbox (thank you, @sol), has solved my problem.