Then go into disk management, and assign the drive a latter again if it still does not have one after the chipset update.
As for your scanner, did you try installing driver in XP mode, in windows 7? That may help. If not, and you want to try to get it working in windows 7 please give me the full exact model and I'll see if I can find you correct drivers that have been proven to work in windows 7.
IDE mode is not needed at all for the SATA controller, and I suggest you switch that to AHCI as mentioned above. You will need to do exactly as I mentioned before you change it to AHCI.