I know its an old post, but I've experience the same problem with a 8 year old acer centrino notebook using windows xp.
When using manual jogging the movement its fine and smooth, but when running the program it stops every second, a short time and continue until finish, annoying.
The way I solve this is changing the LPT1 port properties in BIOS. Before was an EPP port. I changed it to ECP+EPP using a DMA and works like a charm.
Hope this help. See you.