That's a PITA. I also have too many HDDs in my home machine: 6 full time, and drive drawers for 2 more. I went through a similar mess during two periods, one on an NF2 MB and the other on an NF4. My solution was to take certain Seagate drives from my rig. The ones I had problems with were a 7200.8 300GB PATA and a 7200.8 300GB SATA. I originally had problems with a 7200.9 500GB SATA, but tech support was kind enough to provide a firmware update that fixed the issues on my NF4 rig.
I haven't seen any controller compatibility / data corruption / data loss issues with Seagate's 7200.10 series. I feel most comfortable with WD's RE2 series right now... they run cool, have a 5-year warranty, and haven't given me compatibility issues even without disabling TLER.
I'm not saying your Seagates are necessarily causing your problems, just that I've found them to be a bit tempermental on certain controllers. One point: the drives that caused problems on my NF rigs are doing fine on Intel 975 boards right now.
Anyway, you might go through your Event Log to see whether there was anything strange logged before your data loss.