I believe Domino 6.5.4 FP1 has corrected my issues. My mail server hasn't so much as hiccupped since loading FP1. I now have over 41 days of uptime on the mail server.
Regarding the Sametime 6.5.1 FP1 issues, I just received some debugging code from IBM. I will likely put it on after my personal downtime. This is from the technician about the debugging code:
Here is the test fix that requires 6.5.1 FP1 to be installed. Because it prereqs 6.5.1 FP1 (product 5733LST PTF ST67007), that PTF must be permanently applied (using APYPTF) before this one can be loaded.
You will need to edit sametime.ini and turn on logging for the channel operations of the StMux service by adding VPMX_CNL_DEBUG=1 to the [Debug] section.
This will log information to stmux.txt in the trace directory of the Sametime server. We are collecting information about the size of the peer channels table and the resizing of it that is causing the crash. When STMUX experiences another crash, please send in this trace file, as well as sametime.ini and sametime.log. Then delete the existing stmux.txt file and restart the sametime server. A new stmux,txt file will be created and logging will begin again.
Sounds like this will be doing some good data collection!