When the mpg2 is connected it works fine except that i cant run a program. I jumps all over the place and loose steps.  I can jog just fine and even cut at feed speed, but at rapid speeds it makes a very bad grinding noise and looses steps.  Its similar to when your setting up servos and they are out of tune or running faster than spec. The only way i am able to fix the problem is to remove the 2nd card and mpg2. Also, when the c22 is pluged into the 2nd port the pc will hang on boot up, but works fine if i plug it in after boot.
 
Im figure its a conflict with the onboard para port, but not sure how to fix it.

When you say

I can jog just fine and even cut at feed speed, but at rapid speeds it makes a very bad grinding noise and looses steps.

Are you meaning that you can jog and cut  using the MPG or are you meaning the code running is fine but a rapid in code is not when MPG is connected?
 Is it ok if you keep the card in but just remove the c22 (which I presume is a pendant?)

Hood

The MPG2 pendent is connected to a c22 card that converts pins for the 2nd paralell port.  I can use the pendent just fine, but if i run a cnc program it looses steps (esp. on rapids).  When the pendent and 2nd paralell port card  are removed every thing is fine.  Btw, i just reinstaled the port drivers  for the 5th time and everything works.  I still can't boot up the pc with the pendent connected.  Seems to be some bugs between the 2 ports.

Problem came back not sure what to do at this point.

Is it more stable to run a MPG though MOD IO?

If you have the problem with only the port installed and nothing connected then it must be a windows issue I think.
MPG via a parallel port usually works very well, I have certainly never had a problem in the past even though I now use the SmoothStepper on all machines.
Hood