I've heard of this before. What you need to make sure of with WebPosition, a tool that is rapidly becoming obsoleted by personlized search IMO, is to decide if you REALLY need to run ALL of the searches you have queued.
Most of the time people using WPG have about 20 times more queries running than they need to for good
SEO. Lots of folks will take something like Keyword Elite and generate 100s of keywords, feed those into WPG, and let it run all night. Google no likie.
Also.. make sure you have plenty of space between your queries "courtesy waits"... perhaps as long as 10-15 seconds. Yeah, your reports will take a while, but again, you may be running far too many terms.