Flashed BIOS - IDE controller problems

Hi,
I have been having a bit of a problem with one of my
machines, and I was hoping someone could help.
Here's the story:
I flashed the BIOS on my TCommate MB, P2BXA Rev. 1.02,
with a BIOS directly from the manufacturer. It updated
the BIOS from v. 1.01 to 1.06. The specs on the machine
are as follows: PII 400/512MB SDRAM/11GB HDD and 40GB
HDD. When I first booted up after the flash, it
redetected all of my HW. However, the drivers for the IDE
controllers will not load properly. The problems are with
the Primary IDE controller (dual fifo) and Secondary IDE
controller (also dual fifo). The error message is:
This device is either not present, not working properly or
des not have all the drivers installed (code 10.). The
drivers installed are ESDI_506.pdr and IOS.vdx, version
4.10.1998, created 4/23/1999.
Now, I have a CD-ROM and a DVD-ROM connected to the
machine, neither of which are detected (the BIOS picks
them up).
When I click on performance, I have the following warnings:
Compatibility mode paging reduces overal system performance
Drive C is using MS-DOS compatibility mode file system.
(and when I have the D Drive plugged in, the same for D)
Neither of those messages appeared before the BIOS flash.
A little more info on the BIOS flash: AWD modular BIOS
4.51, checked the BIOS string before flashing, and this
was the correct one from the manufacturer.
If anyone could help, I would REALLY appreciate it. I
think I have included all the info needed, but if there's
anything else I should have posted, please let me know.
Thanks