I recently upgraded several systems from 5.2 to 6.0 and we had some problems. We are a test engineering group and we use VxWorks in our systems. During the test process we ftp from a controller board into a linux machine for test authentication. When we upgraded to 6.0 the test fails, to verify I down graded one machine to 5.2, and the test passed again.
Presumably this is a wu-ftpd server bug ... Try the wu-ftpd from Raw Hide on a 6.0 system. There's an RFC931 identd lookup timer problem that is fixed there. You can also disable the identd from the command line -- IIRC, adding "-I0" to the daemon startup will do the trick with the wu-ftpd-2.5.0 errata daemon. Otherwise, I'll need more information. The output of tcpdump on a (small) failed test would be helpful.
This problem appears to be resolved. Please reopen if I'm wrong.