Okay, I'm finally on a computer so I can elaborate a bit more. I think I may have tracked down what's happening. I found another forum with a thread about a pea comb modifier that restricts a pea comb, and I think for whatever ungodly reason, my hens are carrying that. When I bred them with the male from their lines, the combs looked fine. Now with this outside male, these combs are popping up.
Gave the hens a bit of a closer look this morning, but I didn't have much time before work and it was kind of dark. Two for sure look 'off'. Not full-on pea comb off, but not 100% right. How on Earth did I not inspect combs on birds before breeding them? I feel like a dunce. Never occurred to me that there could be this much trouble on a single combed breed, I gave them a glance and that was that.
Anybody have any more ideas or experience with things like this?
Am I right in thinking that if I put the male over any daughters with good combs, this should be gone?
ETA: Here is the only thing I can find about this:
http://www.the-coop.org/forums/ubbthreads.php?ubb=showflat&Number=88595&page=1