This is not quite a bug but is a consequence of current CVS Plugin tagging start policy.

Once the tagging is not part of a build job Jenkins can not consider it in its restart constraints. Therefore when you upgrade Jenkins or some of its plugins, checking the "Restart once no jobs are running" ignores the running (manually started) tagging (if there is no job running in parallel) and restarts regardless of the running tagging, thus breaking the tagging process.