Yup, that happened to me. I was a straight D before the diet. After a couple months on it, I was suddenly having C problems. It's just a normal part of the process for a lot of us, I think... a HUGE part of this is experimenting with SF/IF proportions, supplements, and so on, and it really does take a while to get the balance right, with so many factors. Plus, the hormones could definitely be bothering you still.
I can't even recommend which to increase - SF or IF - because it's such an individual thing, and sometimes the answer is a little counterintuitive. (For example, I require massive amounts of IF to stay stable, even though I'm most prone to D - something that most D'ers would never handle well.)
Good luck, and hang in there!