Ok, I decided to give it one last try. After uninstalling PFE 2 weeks ago I did a reinstall today, everything as admin and outside the \Program Files\ tree. I also switched off UAC in W7, just to be sure.
Maybe it works now but to test I have to compile a flightplan. I convert a xxx.pln and get a PFE_xxx.pln in FS2000/Pilots folder. I run PF2000 and read that plan and compile it to an (supposedly) adventure. After that I Exit PF2000 and try to load the adventure in PFE but it says 'File selected is NOT a Proflight2000 ADV file!'. Tried several plans and same result with all. I checked and those .adv's (in PFE/PF2000/Adv) are the only ones generated.
During previous install I didn't run into this problem. Probably something stupid but don't see it. Any help appreciated.