I'm suspecting the females are dying due to stress or perhaps, as you are thinking, they're getting attacked by the male when you're not looking. Bettas don't generally do well with tank mates, with the exception of females....meaning girls tend to get along ok with other girls. This is usually only true in larger tanks, though, from what I've learned and isn't fool proof. Some Bettas like to "rule the roost" so to speak and won't share their space.
From what I've read about pairing Bettas (male & female), the courtship is usually short and should be approached with caution also. Some males and females won't get along well even when you're trying to mate them.
Bettas are wonderful fish to keep with lots of character and beautiful colors/patterns, but they are still sensitive to the usual calamities that befall fish. I had a very aggressive female once whose death I inadvertenly caused when I introduced some larger, more aggressive tank mates. She was in a 40 gallon and literally got chased to death by some Giant Danios. I was horrified and guilt ridden, but it showed me how sensitive any fish can be to stress.
Hope this helps. Good luck with your fishie!