I found this theory in a Spanish magazine "La Aventura de la Historia", and it said that the story went something like this:
Henry wanted to get rid of Anne, much more after having Catherine out of the way and after Anne's last miscarriage. He needed an excuse, and Cromwell (as usual) was working on it. Then the quick downfall of Anne began, that we all know... But, when Anne confessed to Cranmer, he said that she had told him "a horrible secret of which i can't speak". I can't remember why Weir got to this conclusion, but there where two parts to the theory:
1. Anne was carrying a child which could or could not have been Henry's. Cromwell supposedly convinced Henry about the baby not being his (well, if he hadn't have relations with Anne that was not a difficult task!) and Anne was beheaded on the charges of treason, adultery and wichcraft.
2. Anne was Henry's own daughter, illegitimately born from a relationship between a teenager Henry and Elizabeth Howard (the magazine said this would explain the lack of information on Anne Boleyn's birth!).
I'll continue trying to find the article where i read it!