I also encountered this problem at some sites. I think it is due to directories of removed (or moved) modules or moduleparts. In this case the problem dirs was:
mod/assignment/type/assignmentoffline/
mod/assignment/type/assignmentonline/
mod/assignment/type/blog/
mod/assignment/type/program/
I have also noticed other directories causing problem after a CVS update.
Regards,
/Marcus
Assignment
Assignment module causes cron to stop
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