OK, like allways, I would recommend this: format c: and start over. 
Why? You have done a lot that can confuse a PC: upgrade the OS, 
change the boot drive, added drives, upgraded software (Xplode had it's quirks ...), and so on.

Besides that, it seems you suffer from IRQ issues. 
Therefor: start all over, from scratch.

First: dive into that BIOS and disable what will not be used: 
USB controllers, IDE controllerts, serial ports, parallel ports, 
PS/2 port ... Anything that will not be used. This could save up to 4 IRQ's!

Second: still in the BIOS: assign to the slots the Rex and RT are in, 
their own IRQ's. 9, 10 and 11 are the good ones! RT can share 
with the Rex, but if you have IRQ's enough, don't share. Leave 
the others alone. Do not plug in the Rex and RT boards yet! Simply 
reserve their slots. Put in all other hardware you will be using: 
NIC, Xplode ... Install the drivers for the Xplode 2.11, BUT NOT 
the XPLode software!

Third: install W2k. Very important: W2k will most probably try to 
install as an ACPI PC. ACPI is the advanced PnP system (to assign 
IRQ's and stuff). But because of the lack of proper support at 
this time from hardware, it's mostly a source of more advanced 
problems. So, when asked, do not install ACPI, but install W2k 
as a 'Standard PC'. You can change that afterwards too. Or, disable 
ACPI in the BIOS too, if the option exists. If possible, disable 
all power management in the BIOS too. Test everything before 
proceeding! Check for IRQ assignments! There should be nothing 
on the IRQ's you reserved for the slots the Rex and RT should 
be in! If they are assigned, do not proceed, and check for an 
ACPI installation. If so, remove and install as a 'Standard PC'!!

Fourth: if all is well, start adding the Rex and RT boards together. 
Have the latest 2.8 release available. After rebooting, point 
to the latest 2.8 drivers (unpacked in a folder). After 
rebooting and proper driver installation, install the 2.8 software. 
Again, test before proceeding. If you want to use Premiere or 
MSP with the Rex, install these before installing the Rex 2.8 software!!

Fifth: after having thoroughly tested the workings of RexRT, 
install the plugins: Xplode software, BorisFX, ... Whatever plugin 
software you might want to use: Quicktime, ...


And allways: if at any step like I described it, things do not 
work properly, do not proceed to the next step! Solve the problem 
first! It will not go away by going to the next level! It will 
not be solved by ignoring or working around it!

Good luck,