If using the parallel port on large files, turn off the toolpath display.

Ill run the drive test and let everyone know how it goes. I am not too familiar with the drive test is there something specific i should look out for while running the test?

You ideally want a very flat line in the graph although some small deviations are usually OK. what I would be interested in however is there are large spikes at intervals similar to the interval of the pausing you are seeing.

Other thing you could have a look at is Ctrl Alt Del and watch the CPU usage whilst running the code and see if the CPU goes very high during the pauses. If it does look at the processes and see if there is anything obvious there that could be the problem.
Hood