Jason, there could be a few different things going on. The 'clunking' sound you are hearing is a really good sign that your not getting a good, jitter free pulse stream. Laptops are typically not a good choice as a control computer as all the power saving stuff they put in them interferes with processor speed. There are a number of tricks you can try on a laptop but in my experience the results are usually not very good. I always try to sell folks a SmoothStepper with the systems I sell to prevent them having problems trying to get things running smoothly with a parallel port. On a laptop I would say that a SmoothStepper is mandatory.
I'm not sure how your system is set up (power supply type, voltage, stepper wiring, etc) and what type of speeds your trying to run. The HobbyCNC board is what I would refer to as an 'old school' design. Nothing wrong with it in general, but you just can't get the same performance as with a more modern design. Drivers like the Gecko have midband resonance compensation (adjustable), morphing microstepping (go from 10x microstepping to full steps as you increase the velocity), etc.
With your laptop I would suggest a SmoothStepper, if your in Oz then Peter is your guy. If your in the States or elsewhere I could set you up with one.