i'm not sure i get it ...??
you're miffed because pages on your site other than you homepage are getting more backlinks than your homepage ?
maybe its just because your home page doesn't really work like a homepage in itself ??
its a mix of spiel, faqs, marketing messages, flash content, diary etc ...
you could try to shorten it for a start - keeping only the content that you'd expect to find on a homepage - structured traditionally with good links to all appropriate sections (including title tags) utilising your relevant keywords ...
try to condense things - Google may only read the first few hundred words on a site - that may be why it is able to rank your microsites higher ?? cos it can assess all the content .. wheras your homepage rambles in all directions ..
that's just my thoughts ...