Most parallel ports are not happy at 100KHz and the majority seem to behave best at 45KHz or less. It certainly sounds like the pulse stream is your problem and if so then the SmoothStepper will help you with the added benefit that you will have plenty of overhead to get your motors to full speed without having to resort to electronic gearing.
On my lathe I had to use 45KHz and 2:1 electronic gearing and the fastest rapids I could get were 3,200mm/min. I could have increased the electronic gearing to get faster but I wasnt happy with the slow speed motion with any more gearing. I put the SmoothStepper on, set the gearing to 1:1 and could get rapids of 20,000mm/min. I settled for 10,000mm/min in the end as the lathe is heavy and having rapids that fast were just too frightening
Hood