Depends on how the fans are connected. Oftentimes case fans are hooked up direct to the PSU and thus aren't controlled by the Mobo and it's headers' controls. Also, considering your idle temps are a bit high as well (though not entirely unusual - my CPU runs about there too, but I seem to have received a bit of a near-faulty chip, as it runs significantly hotter than reviews/benchmarks have shown for mine) it likely couldn't hurt to redo your thermal paste. Especially considering that cooler should be perfectly capable of keeping those temps down.
Also, having more exhaust than intake, IIRC, isn't usually a good thing. You end up drawing from cracks in the case and from the air around the case, as opposed to the (hopefully) cool air from the front of the case. Might want to consider revamping that part of the layout.
Edit: After re-reading your last post, I think thermal paste might be your first stop to check. Fairly cheap to do as well. It just seems that by all other accounts, you have good system building principles in place for the most part.