It never had this problem before? Your description of the behavior sounds as if it's having trouble auto-detecting. What happens when you tell the BIOS to auto-detect drives? (try several times) Same big pauses?
New drivers wouldn't cause this (they aren't active yet), but bad geometry settings, cabling (including power), jumpers, dying component, or a flaky battery (as Ripsaw suggested) could. The erratic nature really points to something wrong at the hardware layer. Unless I'm misunderstanding your description, of course. San Diego? Impact damage from your house sliding down a hill recently?
What orginally motivated you to do anything in the BIOS? RAID? Do you remember all the changes you made?
May as well go for the gusto. What mobo brand/model & BIOS revision? I'm tempted to ask you to enumerate all storage devices, plain IDE, SATA, SCSI, whatever, but then you'd think I was stubborn.