I have an elder statesman Pro. This morning he restarted himself to a folder with ? Restart was "on his own" no one touching anything. What was that all about?

A couple months ago, I went to work on my Mac Pro. I found that there had been an apparent restart - for which I was not present - and the screen now was blue, with a folder on which was a ?, as in the Pro could not find a startup folder.
After an agonizing morning of trying various things, I finally got the computer to start on a DVD. From there I could access my hard drive and used Time Machine to go back a week and restore everything. Shortly after that, I got my heart back into normal rhythm.
This morning, at 0600, while I was doing something completely un-computer related - the computer being untouched since last night - when my Pro shut itself down, then restarted itself. Again, the startup was interrupted with a ?folder, "I cannot find my brain this morning" icon.
I shut the computer down completely and left for a couple hours. I have now restarted the computer, feeling like, although I would lose a couple hours work, at least I knew the situation wasn't hopeless. To my surprise, the Pro has started up as normal and all things seem normal.
What is this "I will simply restart as I wish" routine - seemingly at 0600 - and why can he suddenly not find his startup routine?
As a possible clue, I offer the following:
While I did not see the original restart, I believe it too was at 0600; I was in the office shortly before that time, left, and returned about half an hour later. I have the computer set up to awaken and grab my email at 0600, so I can sit down and go to work.
Also, I have noticed since the first incident, when the computer awakens in the AM, I frequently have to reconnect my wireless mouse and/or keyboard. Sometimes I actually have to re-add them to my bluetooth list. Sometimes they remain listed as favorites, sometimes not.
This is an older Pro, dual-core Xeon processor, running 10.6.8 - mostly to accomodate some of my software.
Any ideas are appreciated.
Thank you,
Cheryl

Temperature Monitorhttps://www.macupdate.com/app/mac/12381/temperature-monitor
http://www.bresink.com/osx/HardwareMonitor.html
SMCFanControl 2.4+
https://www.macupdate.com/app/mac/23049/smcfancontrol
UPS
http://www.amazon.com/CyberPower-CP1500PFCLCD-Compatible-1500VA-Tower/dp/B00429N 19W/
Metro Vacuum ED500 DataVac 500-Watt 0.75-HP Electric Duster 120-Volt
www.amazon.com/Metro-Vacuum-ED500-500-Watt-Electric/dp/B001J4ZOAW/
X1900
http://www.xlr8yourmac.com/Graphics/X1900XT_Overheating/ATI_X1900_artifacts.html
http://www.xlr8yourmac.com/Graphics/radeon_X1900XT/X1900XT_dust_buildup.html#sto rytop
ATI Radeon 5770
http://store.apple.com/us/product/MC742ZM/A
http://www.amazon.com/Apple-ATI-Radeon-5770-MC742ZM/dp/B003Z6QH6M 
http://www.bhphotovideo.com/c/product/726537-REG/Apple_MC742ZM_A_ATI_Radeon_HD_5 770.html
How To Install and Remove Memory Mac Pro
https://support.apple.com/kb/HT4433
2x2GB FBDIMM DDR2 667MHz @ $32http://www.amazon.com/BUFFERED-PC2-5300-FB-DIMM-APPLE-Memory/dp/B002ORUUAC/
Resetting the System Management Controller (SMC)https://support.apple.com/kb/HT3964

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