I found the C-One mailinglist (had it bookmarked before, but apparently forgot about it because I hate the yahoo mailinglist system) and this post:
"Oh sorry thats right. Thanks chris!
here the new steps:
1. Make a CF Card with Partition table (Superfloppy not supported by all parts!)
and format the first Partition with FAT16 or FAT32,
I recommended this tool:http://panasonic.jp/support/global/cs/s ... ter20.html
2. expand the "NewbootV201.zip" into the root,
3. delete the minimig_pal and the Minimig_ntsc folder from c1dcores,
4. expand the "C1minimigV201_build.zip" and copy the files from the
"v2.01" into the root from the CF,
5. copy a "Kick.rom" into the root folder,
6. put some .adf files to the root folder.
Now should the Minimig Core work on the C-One.
So apparently it was a problem with the CF-card after all, after reformatting it with the panasonic util and installing everything again, it finally works. (Edit: Also ps/2 mouse, which didn't work before for some reason.)