Yesterday I worked on the backup problem some more - ran several tests. When using the new binary sent by tech support for troubleshooting, the tests all worked fine - no errors. Of course, the logs quickly grew to over 150mb, and the speed was quartered. I put the original binary back in place on the unix server, but left the new one in the w2k server - ran more tests, all OK. Last night I ran a full backup and it worked fine!
After speaking with the tech, we are going to let it run normally for a few days and see what it looks like Monday. If the backups are working fine now with the new binary, they will turn off all the massive logging, otherwise the logs would quickly take up all the room on the drive. I think it is slightly amusing that after 6 months of hassles, the remedy was a newer client agent - that tech support had the whole time.
Of course, if the error pops up before monday, we will be in the same place we were before, and the troubleshooting will continue.