Gigabyte 7dpxdw-p Silicon Image 3114 Boot Win2k3 sata Raid 1

Ok, here is my problem. I cannot get windows to boot off my sata pci controller with all my other controllers and drives set up. If I disconnect all the other drives, windows will install onto my two 320GB mirrored drives fine. Once I hook up the other IDE and SATA drives however, I get a “No Active Patitions” error. And If I try to install windows onto those same two 320GB mirrored drives, windows wants to put startup files onto the drive connected to the first IDE port on my motherboard, which it says it can’t do because I already have a dynamic partition taking up the whole drive, with files I’d like to keep.
I have tried changing the two 320GB mirrored drives to ports 0 and 1 on the Silicon Image 3114 to no avail, and I need all the other drives to be hooked up because this is my main file server.
Thank you all in advance.

System specs;
Gigabyte 7dpxdw-p with F5 Bios
1.5 GB 266mhz DDR 2100 ECC REG Ram, 3x 512MB Sticks
Radeon 9000 AGP Video Card
PCI Slot 1 - Empty PCI-X slot
PCI Slot 2 - Silicon Image 3114 PCI SATA controller with RAID bios version 5.4.0.3
PCI Slot 3 - Intel Dual Gigibyte NIC, PCI-X
PCI Slot 4 - Silicon Image 3114 PCI SATA controller with RAID bios version 5.4.0.3
PCI Slot 5 - Promise ATA 100 TX2 PCI Ide Controller card with bios version 2.20.0.15

If you want to add drives to the SATA PCI controller, you need to install the driver most likely.