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Crosshair III eSATA question

Last response: in Storage
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I am embarrassed to say I am in IDE mode, i figured my motherboard would have just left in in AHCI. THis next part of my question goes out to anyone who has switched to AHCI mid operating system. I changed the two values in the registry to allow for AHCI installation, and changed the BIOS. When I then load into windows i can tell it is installing new hardware but then i get DCOM and Plug and Play services terminating unexpectedly and a forced reboot, even when i disable automatic restart on system failure. Does this mean I have to reformat or is there something else I can do?
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See i follow those instructions and its a no go, I get DCOM Services was unexpectedly terminated as well as Plug and Play Unexpectedly Terminated forcing me to reboot. It becomes a loop until i switch back to IDE

Basicaly to clarify, the OS is on a hard drive (C) but for some reason for the OS to boot Hard drive (E) has to be plugged in. IF it is not i am told that BootMGR is missing. I do no run a raid obviously (or at least i think its obvious) because it is stuck in IDE mode and the two hard drives may both be seagate but differ in size and model (if the old RAID rules are true). I think im going to have to go down the formatting path because of some start up issues i had before i tried modifying anything, which from the limited knowledge i have may be caused by this weird breakup in windows files. Any advice would be appreciated, i would prefer to avoid reformatting... Sorry this thread has turned into so much more.
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