I think this turned out to be a hardware issue. I'm not certain if it was a specific piece of hardware that was malfunctioning, or if it was some kind of intermittent compatibility issue. I suspected hardware after the machine started randomly locking up. I had an identical machine, so I swapped the hard drives into that one, and it had weird issues as well, but my LAN interface (which was a VLAN) wouldn't work at all, so I had to take the add-on NIC card out of the original machine and put it in this one, even I just replaced an identical card. Then it worked, but it still had random lock ups and such. From there, I migrated my whole setup to a VM, and I've had no problems. So either it was the hard drives, the original NIC, or both machines have some internal hardware issue.