Hmm... While it would require a bit of work on your end, I would try it out on full stock and verify it works as it should, and if it does then verify again after flashing either the kernel or the rom (but not both). Unless other more knowledgeable folks have a better idea of what could be at play here, it's hard to say what the problem could be (or where one should look to figure it out). Let me know if you find anything out.
If you like what I've done... I like sammiches so feel free to buy me one