It's mostly an issue of consistency of use. In the case you describe, most of the best links to your site are using the www.
But a few people are using linking without the
www., and those linkers have lower pr, so google treats the two urls as different sites and assigns them different pr.
If no-one at all linked to you without the www, google sometimes seems to assume the www and non-www version are the same site, and gives them the same pr. (there could be other explanations for this effect...)
Not always, tho, one will often see one version with all the pr and the other with pr0.
Those domains that have equal pr on both versions usually have a broad base of incoming links using both www and non-www, giving both versions pr.
The usual approach to this is to try to make sure everyone links to you using the link you want to emphasize. Some choose the www, some the non-www.