Flashcut Woes

So this is a really weird set of instances. I have 2 complete
flashcut setups. One has been running very well off of a Pentium 3
(P3), and I had previously run it off of a Pentium 2 (P2).
Rig #1 runs well off of a P3. I went to start up rig #2 with a P2,
and I experienced some weird signal generator behaviour. It would
stop working and start flashing all LEDs indefinitely until I rebooted
it, and after a reboot it MIGHT work for a few seconds before locking
up again and flashing.
So to isolate the problem I tried it on the P3 from rig 1. It worked
flawlessly.
I replaced the faulted P2 with a P4. This time the signal
generator...running off of a serial port, acted like it was on, and
worked...but did not move motors. I do not think this is the driver
box. This only happens on the P4. Something is happening in the
computer to not make the motors work, because my driver box is in top
notch.

At this point, I'm having it work w/ certain serial ports. It works on
my P3 and it had worked on a P2. Is there something in my P4 that can
cause this behaviour... Are the serial port setups different on newer
motherboards than they were on older ones. Has anybody had any
similar problems?

Thanks in advance if anybody can be of some help.
Brian