strange recognition/non-recognition/backward recog. of HD

[rombolo11]

So i just got a new custom comp. I've been trying to set it up and hit many snags and am beginning to narrow down the problem. I feel the problem is in the BIOS and this is why:

I have 6 SATA connections: 4 are SB600, numbered 1 through 4; and 2 are JMB363 numbered 5 and 6. Now when i plug my WD 250gb HD into SATA-1 it come up in BIOS as Primary Master, SATA-2 is Primary Slave, SATA-3 is Secondary Master, and SATA-4 is Secondary Slave. However, when i run through the start-up sequence (all those words and numbers across the screen before it gets to the OS loader) it says No HD found or something like that. If i connect the same HD to SATA-5 or SATA-6, it will display that a 250gb WD HD is found to load from, but this HD does not show up in BIOS. Interesting, huh? Well here's the kicker. If i plug in the HD to SATA-5 or 6 and run through a clean install (this is a new HD) i am able to install the OS on the HD fine. If i plug the HD to SATA 1-4, the OS installer does not find a HD ( i find this out because when you search for the root path to load the kernal, it can't find it because it can't find any hard drives). So here is what i did, i plugged the HD into SATA-6, ran the install, when it finished i unplugged the HD and attached it to SATA-1. This seems like it should work, however the once it gets loading the OS stalls at the same point.

Does anyone have any ideas? This is all new stuff, very good, i can get the exact info but this seems like it doesnt matter.

Thanks

[edwin]

For the SB600 SATA connection you need to feed windows a driver file from floppy during the F6 stage of the text-based setup where it asks for additional drivers.

I suspect the JMB controller (SATA 5/6) is using some sort of IDE compatibility mode which account for windows finding the drive.

In the boot.ini file all those drive positions have different designations so if you move the disk around, windows cannot find the drive it wants to boot from initially anymore.