Don't Know Why

I don't know if anyone is reading this but I'll post it anyway.
When I first installed Win 7 Home premium 64bit, the only thing I made sure of , in the BIOS, was that my first boot drive was my CD/DVD then C. I did some reading in regards to AHCI and how it could help in performance. So, being nosy I decided to try it. I found how to change from IDE to ACHI after installing Win 7 and followed the instructions. After changing over I did some looking. I found that 1. Using DISKPART, my C drive, Disk 0, was now Disk 2 and my Disk 0 drive was now D drive. I also checked in Computer Management and sure enough Windows was reporting the same thing. I didn't change the Registry entries because after bfk had tried that and it didn't work so I didn't bother.
2. I decided to revert back to IDE and reversed the process just to see what would happen. After doing so I found that my C drive was now Disk 2 and D drive was Disk 0. I switched my connectors again, C on 0, D on 2 and E on 4 and my CD/DVD on 1 and found C back to 0 again. This was not done just by reboot, I shut down and did all checking. The BIOS and Registry all report the correct boot drive, yet when AHCI is enabled C is knocked out. It looks as if there are a lot of things that contribute to this annomily and it's gonna take a lot of people to figure it out.

I'm watching as well. It's not life threatening but under my skin.

Whats really strange is the fact that after AHCI was initiated I checked the BIOS and C drive was still listed as first drive even though Windows reported it as disk 2. I have to apologize for not mentioning that before, I was doing a bunch of other things at the same time. Sorry bout that.

So what did you do to fix the problem?

I don't understand. I have had my stuff straight, other than using AHCI, for about two days now. I have shutdown, restarted, all that stuff and everything is still the same C is still 0, I've even turned on my external drives and nothing has changed. There has to be an answer. I did notice on one of my external drives, Windows reported that "F" drive which is external was an "Active" partition, so I ran DISKPART-clean all and now its just a Primary partition, none of yor drives is being reported as "Active" other than C right?. I'm going to make a stab at this but do you have AHCI enabled? If so that cold be the problem. Now I know you're gonna say no way but, what happens if your 1tb drive is disconnected? I'll bet you've tried all that right? In all honesty, when C was 1, it booted just fine and I don't think it will make much difference if C is 1, it just matters if you have to re install or have to repair, then you just disconnect the other drives,which you shouldn't have to but you just might have to live with it. Man, what a bummer.

I still think the rationale put forward by Dwarf looks reasonable now
Diskpart / Disk Management vs the BIOS

ASUS have it as one of their FAQs and don't seem to have a solution.

Apart from it being a nuisance what do you see as the main consequence?