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I've used AHCI with no problems. Thought IDE prevented TRIM firmwares from working properly?
If you switch back and forth between AHCI and IDE without reinstalling you'll get that issue. Same goes for traditional drives. The two modes address differently so you'll have to use a tool for MBR repair to get windows to recognize that you've changed things. Otherwise it just assumes that the hardware has changed and has no clue where to boot from. If that's the case you could use a usb linux distro to take care of it such as PartitionMagic.
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