Chris-

After reading your post, I realised that my data also had subfolders which I had seperately put into the converter. After converting my whole datafolder at once, the problem seems to go away. I guess not every required file was stored in the correct subfolder. 
 
If something still doesnt work I'll let you know, but for now it seems that I'm good and can start my analysis.

Thanks again for your immense help!

Lars