MSI 6378 Disk I/O issue

I recently updated a PC installing an MSI 6378 Combo motherboard in
the process.

While the machine is basically stable, the disk performance is poor.
Configuration:

Athlon 1700 XP @154
256 Crucial 2100 DDR
WD 20 Protege 5400 HD
BFG TI Gforce 4200 RI video card
Toshiba 16X DVD
MSI onboard audio and ethernet interfaces
Windows XP Professional (clean install on new HD)
Latest BIOS and VIA drivers

Symptoms:

System will not boot when disk is strapped MS and cabled accordingly
System will only boot from disk when strapped CS
System can only play games when IDE 0 is cabled as slave
System will not boot from floppy under any configuration
System runs very poor disk benchmarks (Pc Mark 2002) ie. values or 200
to 400
When disk is cabled as slave benchmarks increase (sporatically) to
500/600.

I don't care about the benchmark values, they are only indicative.
The system has to be cabled as IDE 0 / slave to play games at all. If
IDE 0 is cabled as as master while the system boots, it is unusable
from a gaming perspecitive.

This was a working setup that used to work well under Windows 98 SE
under FAT 32( with a different drive). As stated, the disk drive was
new ( a WD RMA claimed to be an "upgrade")as was the XP installation.

My surmise (in order):

The HD is crap (in spite of what WD says)
The BIOS/MB is crap
I don't know what I'm doing

All insights and links to resources are much appreciated.

Joe