I have been having issues with my mid-2009 Mac Pro ever since I installed Mountain Lion. First it was intermittent kernel panics; I did some research and found that this is an ML bug that's triggered by having multiple Nvidia GeForce 120 video cards. Nothing I can do about that but wait for Apple to fix it.
Then I started coming to my desk in the morning to find the computer shut down. I could tell from the logs that it happened around 6:00 am, but I could not tell why - the messages just before the crash were different every time, and usually were not error messages.
The only thing I know of that runs in the wee hours of the morning is my SuperDuper! backups, so I commented all of those out in crontab. I thought that had fixed it, but this morning I realized that actually what that did was change it from a shutdown to a reboot. "last" shows this:
janine ttys004 Mon Apr 8 05:53 - 11:20 (05:26)
janine ttys003 Mon Apr 8 05:53 - 11:20 (05:26)
janine ttys002 Mon Apr 8 05:53 - 11:20 (05:26)
janine ttys001 Mon Apr 8 05:53 - 11:20 (05:26)
janine ttys000 Mon Apr 8 05:53 - 11:20 (05:26)
janine console Mon Apr 8 05:52 - 11:20 (05:27)
reboot ~ Mon Apr 8 05:52
janine ttys004 Sat Apr 6 06:22 - crash (1+23:30)
janine ttys003 Sat Apr 6 06:22 - crash (1+23:30)
janine ttys001 Sat Apr 6 06:22 - crash (1+23:30)
janine ttys002 Sat Apr 6 06:22 - crash (1+23:30)
janine ttys000 Sat Apr 6 06:22 - crash (1+23:30)
janine console Sat Apr 6 06:20 - crash (1+23:32)
reboot ~ Sat Apr 6 06:19
The crashes due to the video cards cause Kernel.panic files to be written to /Library/Logs/DiagnosticReports, but these reboots don't leave any trace behind other than the above.
There is nothing running from crontab now. The only things I can think of that run automagically are Dropbox sync, Backblaze and Time Machine, but those run several times a day, and it seems unlikely that they would only cause a reboot at a specific time of day.
I tried to run the Apple Hardware Test but was unsuccessful. Holding down D while the computer boots does nothing, and neither does option-D. I even switched from wireless to an Ethernet cable and running the test from the Internet still did not work (by which I mean the system just boots normally, with a slight delay which is presumably when it's looking for the test). I do have a wired keyboard so it should be getting the keystroke at the appropriate time.
What else can I do to track this down?