Under Control Panel > System > Advanced System Settings > Advanced tab > Settings button there is a checkbox for Automatically Restart. Uncheck it. Ironically you may need to restart the server for it to take effect.
What I'm led to believe is along the same lines as what Phil McIntosh posted. You have almost 6 GB of RAM but is it all allocated to the VM that is running MAS?
More importantly the Intex Xeon E5606 processor by default has 4 cores (quad core) and a server system will have either 1 or 2 physical E5606 processors installed (meaning up to 4 or 8 total cores) .
Now how many users are running MAS? I have a client who just very recently IT virtualized their physical box into a VM (VMWare 5.1 vSphere) and for 1 week their symptoms were very much like you described in your post. Their 20 users would be running okay then slow down to a crawl. Same with the dozens of business alerts they run and same with the network printing done off that server. When I got to take a look, pvxwin32.exe, das_svc.exe (business alerts), jqs.exe (java quick starter), and other stuff were all spiking the CPU - not anyone in particular and nothing had changed from MAS operational point. It was happening at night even when nobody was in the system and only Biz alerts were running. They would reboot and problem goes away temporarily.
I saw the root cause which was prior to virtualization their box (which coincidentally was running EXACTLY the same E5606 but as a single CPU - total of 4 cores) and with a total of 4 GB RAM (can't go higher on Server 2003 32-bit). They were okay for the most part with this although the RAM was insufficient at times. But when IT virtualized it, even though the host system (which was a brand new screaming 2012 server they purchased) had ample processors / cores to spare, they only allocated 1 processor with 2 cores to the MAS guest system. I asked IT to give them back at least 4 cores and everything went back to normal.
So like Phil said, you want to ask:
* On the host system how many total processors/cores and how much total RAM
* On the guest system running MAS, how many processors/cores is allocated and how much RAM is allocated
I hope this E5606 is in the dual CPU configuration (8 total cores) so they will have additional to spare.