I can think of one reason why this may happen, although I am not sure if this is the case with your sites.
Having rel=canonical on the .net page that points to .com page might be the reason. I have not tried/seen this cross-domains, but I have experienced this with rel=canonical within the same site.
I had a page that had rel=canonical on one of inside pages mistakenly pointed to home page. The PR of inside page showed PR of the home page and clicking on "cached" in the toolbar brought home page content (and not inside page).
I do not know if you use rel=canonical, but if you do, I would check that .net page does not mistakenly have rel=canonical set to .com page (in case that the same can happen with cross-domain rel=canonical).