Please send us some process snapshots the next time it goes wrong, and we'll see what's happening:
Note that there is at least one report of Folder Marker (version 3) causing File Explorer's context menus to break as well:
https://shellfix.nirsoft.net/fix_shell_problem.html?id=238&dll=ShellExt.dll
Also note that applying colors to folders is built-in to Opus, although if you've set hundreds of colors using another tool then it makes sense that you'd want to continue using that one, of course!