If the BIOS is set to AHCI, Windows isn't showing any RAID adapters in Device Manager and only MSAHCI, then I would think that going into the registry and setting services like iaStor* to service start type 3 (manual) should be enough to take Intel RAID out of the picture.
Though situations like this are why I would have advocated nuking it from orbit to begin with - going from a single HDD setup to another and cloning is fairly risk free, but from RAID to a single SSD is a heck of a jump. Yes, it's more work to begin with, but then you're not scratching your head over a bizarre problem and wasting just as much time in the process. Perhaps I'm pessimistic but it's just not worth the risk.
(Not having a go at the OP)