Unless you are mis-typing, or I am missing something, you still are off by a factor of 1,000 on your set resistor.
For the 540, your set resistor should match your motor's draw amps times 1,000. So if I remember right your motors in series draw something like 2 amps, which would call for a 2K (two thousand) ohm resistor.
I'm no expert in electronics, but it seems to me that a 3.3ohm resistor in this application is equivalent to not having a resistor on there at all. I can tell you from my experience with my Gecko 203v drivers that they are very sensitive to having the correct resistor. Bumping and stalling is the symptom of the wrong resistor.
As to your computers, you might check that there is no software polling the parallel port as that could cause the rhythmic bumping that you are getting.
Look for things like printer drivers, antivirus, spoolers, etc. that talk to the parallel port. Make sure your parallel port is set to the highest communication level in the computer's BIOS. If it is set for a printer, it will likely cause trouble.
Other things to watch out for: wireless anything, network, keyboard, Xbox360 controller, phones nearby.
Again, not being a electronics whiz, I would still have to second Hood's comment that the caps may be more effective on the drivers rather than the power supply. I have them in both places, calculated, again as Hood suggested, based on the motor draw.