I have a backup server that is less stable than my other workstations - not good!

My backup machine has 6 internal drives and on the 4 drives (all 1Tb Seagates) I frequently get file system errors. I have no log of what happens. I don't know where to start. If I reboot then the system checks and is able to repair the errors. Though with 2 of the 1Tbs in a 1.8T LVM it takes a while.

Of note - these drives are on two PCI-E Sil 3132 based cards (2 drives per card)

I had another issue last night though with an external USB drive...so I'm wondering if it really is this card or if it's the system. I am moving my data out of the system to rebuild it, but am fearful of this happening again.

Any place to start or logs to examine that might shed some light.

You should be able to see messages in relations to hard disk I/O errors on the terminal screen.
If not there might be messages in /var/log/messages.
Do you have a RAID configuration? (Hardware or Software?)
Did you run file system checks on each and everyone of them?
You can also force a disk check on shutdown using the -F option.

I've replaced the two cards in favor of a single Highpoint RocketRaid and had to go back to Centos 5.1, but it's been very smooth since rebuilding the system. I am now however having the same issue...just on a USB drive now.

After a few days of the system running the disk becomes unusable and an "ls" results in...
"ls: reading directory .: Input/output error"

I cannot double click the mounted disk from the system GUI either. It just gives a generic err...wait...now it works.

Hrmmmmm...what do you make of that. I just was going to type the message and now, without a reboot or filesystem check, it just works. I do have a bad sector error on this USB drive as reported by /var/log/messages "sector 12375"

I have tried to use smart data to run tests, but this USB drive doesn't seem to support that. Any ideas?

Bad sectors are usually a sign that your Drive should be replaced asap.
If you have a spare Hard Disk you could probably insert it into the USB Case and try it.