It was because a new cronbase was pulled. This is fixed in fcron 3.0.3, as it now uses a separate directory (/var/spool/fcron). Portage does the migration itself, you just have to etc-update (or whatever else you use), restart fcron and delete the old /var/spool/cron/fcrontabs.

Problem solved, but I don't know if it was only a problem at my computer or if it is a common problem.
/var/spool had wrong permissions (drwx--x--- 3 root cron). They worker for the former versions, but not for the actual one. But not after the latest changes with fcron.

There seems to be a bug with the ebuild of fcron-3.0.2 .
When I tried the command "check_system_crontabs -v -i -f" (or more generaly: If I try to create new fcron-entries) I got an error message I do not have the right permission.

After installing fcron manually (with the source-files in "/usr/portage/distfiles") the error was gone.

My time at the moment is quite limited, so I just leave a note here, maybe someone else can post a real bug report, if he has the same problems.