The system used to work fine. The problems started after I swapped computer cases/power supplies. I thought maybe I damaged the drive somehow during the move, but I get this problem on multiple drives, multiple cards, multiple cables, multiple terminators. I'm thinking I'm either really unlucky and have multiple bad drives, or there's something wrong with the power supply. Thing is, this current power supply was powering a modern G3258 system before hand without any troubles.
Details: VS440FX board w/ Pentium Pro 200 512k, Adaptec 2940u2w w/ ultrawide cable connected to an SCA adapter, which connects to the drive (original was a 36GB Cheetah, replacement is a 9GB Compaq-labeled). The card also has a Pioneer slot-load DVD ROM drive connected via 50 pin cable. I have tried completely removing the optical drive from the bus to see if it made a difference. All the cables I tried have LVD/SE terminators on them.
In response to derSammler, these LVD drives can be connected to an SE bus. They just run in SE mode at 40MB/s instead of 80. But doing that didn't help as I get the same problems.
But I think the key point I left out was that all of this did work right, and worked right for a long time until I swapped cases/psu's.