I recently discovered an upgraded version of the BIOS for my board, and flashed it. But it causes every HD except for my first to not be recognized as a BIOS physical disk. Instead of BIOS disks 0x80, 0x81, and 0x82, I only get 0x80. This is true for both BIOS versions 1.A and 1.B that I tested. BIOS versions starting with 1.9 included a PXE boot-rom for the on-board Via Rhine II ethernet, and as best I can figure out, is causing the problem.
My three HDs are all connected to a Promise Ultra100 TX2 PCI IDE controller, and up until this recent BIOS flash, have never caused an issue. I have four CD-ROMs on the motherboard IDE channels.
I have flashed back to BIOS 1.7 for now, but would like to use the "core" from the newest BIOS 1.B version, minus the PXE boot-rom. (Because it contains stability fixes for my ATI AGP 8x Radeon card and USB issues.) BIOS version is AMI, not Award. Most of the guides for "modbin" hacking are for Award.

More details, my thread on Anandtech: http://forums.anandtech.com/messageview ... id=1418656
My thread on StorageReview: http://forums.storagereview.net/index.p ... opic=16596
MSI BIOS download page with version 1.B: http://www.msi.com.tw/program/support/d ... 362&kind=1