Hehe, unfortunately I'm the only one here with the passwords to the thing, plus I'm the only one who's brave enough to fool around with Linux. I've made tremendous progress (started at the beginning of the year as a complete Linux n00b), but I'm still not even close to being an expert.
I had been fooling with NagVis a few months before my vacation: I believe the combination of MySQL, Nagios and NDO2DB causes quite a bit of disk activity and causes the virtual machine to slow down somewhat, but it wasn't entirely intolerable. Maybe that had something to do with the extreme slowness when I got back, but I can't be too sure.
I did use the opportunity to upgrade my Nagios version, but the install process didn't fix the startup procedure.
How can I get into the system config and find out what exactly the OS is trying to do when it starts the Nagios service? Because, like I said, I can manually execute Nagios and NDO2DB and it works fine. Maybe I need to redo the commands / user settings for the service startup?