One of our team members upgraded his console to 6.5.4 while the server was still at 6.5.3.1. We have three separate environments and had a rather critical issue occur this morning. When he logged into one master server after logging into another, some jobs from the first environment appeared in the second as "Unknown". Not realizing they were actually not part of the current system, we decided to cancel the jobs.
Later, after logging back into the first environment, we discovered that the cancelled jobs were actually Lotus Notes backups that we had been running for approx. 16 hours already on a master server we weren't working on. We switched between the 3 master servers repeatedly, and there were quite a few job spillovers that showed up between the environments.
We're upgrading our master servers now. Be wary if you are performing a tiered upgrade between your master servers and administration consoles.