We have mostly gotten the fcntl() locking problems under control as far as I know, however the safest solution is probably to find the patch that uses dotlocking instead (I believe that such a patch exists, or existed at one point, and I know that at least one of our users reported success after applying this patch).
Are you seeing this error consistently, or just sometimes?
I sent a quick couple of test messages on the mail machine itself, and they went through just fine (no errors in the procmail log) - and running bogofilter by hand on them worked ok too.
plunder:~$ ./bin/bogofilter -v < /home/iskunk/Maildir/new/1088641156.21936_3.plunder
X-Label: ham, score=0.009469
I also did an strace on this, and verified that the fcntl() function seems to be working properly. The problems we were seeing before were intermittent and hard to track down, though.
Removing the lock on the procmail recipe that invokes bogofilter doesn't help, does it?
When I used bogofilter, I just did:
| [bogofilter commands]