I am pretty sure that this is because Google sees different subdomains under the same domain (ie. a.example.com, b.example.com) as different websites, and so if you got a link to a.example.com, maybe a.example.com's pagerank would improve, but example.com's pagerank will not improve.

This is why choosing one main domain for you website (either www.example.com or example.com) and 301 redirecting all requests from the one not chosen to the chosen one is recommended.