In which case, sorry but I'm out of ideas at the moment, other than suggesting (if you;ve not already done it) checking the Windows event log to see if there are disc read/write errors logged, running checkdisk on everything and seeing if any drive's SMART is reporting any problems, especially the new drive.
Just because a drive is new doesn't mean it isn't faulty......
A switch to AHCI shouldn't in itself cause problems as far as I can see - I've done it myself on this computer (I failed to notice IDE was enabled in the BIOS by default) with no ill effects on anything whatsoever.