I've run into some instances where files deleted in CVS have not been deleted on the buildAgents. I have looked at the buildAgent/work directories and see the files still there. This has happened with certain files on multiple agents, so it isn't just an issue of one of the agents acting up. I can see the files as being deleted in the changes log.
This is with 4111, running on RHEL4, CVS 1.11.17. Is there a known issue like this? I will try and delete a file and captures the cvs.output logs for it. Let me know if there is anything else that would be helpful.