Plug it into another SATA/PATA connection and see if the problem persists, make sure you turn on the connection in the BIOS. It sounds like a seek error. Copy all important data ASAP and contact Seagate for an RMA.
Different controller worked. I think I had both plugged into the RAID Controller (only two connectors), and I stopped using RAID a while ago. It's plugged into the other controller on the motherboard (has 4 connectors) and it works like it should now.