Solved....
What happened:
I'm not a programmer but as far as I can understand does reaper use symbolic links* to redirect to AppData/Roaming/Reaper. Something went wrong with these links.
So after de-installing Reaper, although absolutely invisible to the OS, the Explorer or even the "dir" command, the C:/Program Files/Reaper folder and it's contained links were never really removed, only made absolutely invisible.
I found out by chance, when trying to save a Reaper configuration file. In the appearing file selector box, I suddenly could see and eventually erase the invisible files and folders (or links?).
After a lot erasing, installing, de-installing again, renaming of folders and so forth I ended up with a valid Reaper installation again. When I try out a theme now, it is correctly stored in AppData/Roaming/Reaper.
What a weird problem and what a weird way to spend a Sunday afternoon....
*Don't know if they are called so in Windows, in Linux they are. It's the same mechanism that is used to redirect calls of older programs looking for "Documents and Settings" to the new place where this stuff is stored: AppData/Roaming.
Last edited by StefanMax; 11-09-2014 at 09:01 AM.
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