Especially with P67 but also Z68 and X79 yeah its a smart idea to use the latest BIOS. Further, Intel is the best choice with ALL SATA drives. Marvell is a lot slower and less reliable. The fact that you moved the SATA ports forced Windows to rewrite the registry entries.
Two days all depends on the root causes of the problems. If it was a 'shutdown' (BIOS typically) vs any BSOD (OS typically) then sure the BIOS update was the root otherwise other than 41/63's (BIOS/MOBO) in Windows Event Manager then the registry was the root cause.
Assuming you're running in AHCI or RAID make sure that both Start values = 0
ref - http://support.microsoft.com/kb/922976
Manually verify and change or run 'Fix It'. In IDE mode which I do not recommend the Start values should = 3.