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my guess is yur rank 3 pages get lot of visitors than yur homepage.it can happened if people maybe come direct to those page instead of the homepage.th
Good does not give PR based on the number of visitors a page gets. There are around 200 factors (based on patent info and stuff from Matt Cutts) that get looked at.
It is likely that your homepage is not seen as 'relevant' to searches and information that people are looking for, however your 'internal' pages contain some good information which should be served up to people. It is all relative though as if the info is very niche / specific then the number of potential results is less and thus you have more relevance 'weight'.
The other possibilty is that your homepage is on more than one url
e.g. notrealdomain.com and notrealdomain.com/default.asp or notrealdomain.com/index.html etc Visiting one may show a PR and visiting another may not.
Finally, PR means jack all as mentioned on this post earlier today.