Changed a bunch of settings basically making sure that the speakers/headphones were hard set to speakers/headphones and that the microphone was hard set to the microphone in Windows Sound and in TS3. This slightly helped. I then plugged the headphones/microphone into the rear jacks again, and this has fixed the issue for now. Problem is, the headphone amp isnt on the rear outputs. One of the big selling points for this board over the hero was the sound card and the headphone amp, which both are an issue if I use the front audio jacks.
ASUS Maximus VI Formula | Haswell i5 4670K | 8GB Kingston HyperX Beast
ASUS GTX770 DCII | ASUS VG278HE 27" 144Hz | OCZ Vertex 4 | Corsair 900D
Logitech G15 | Mad Catz R.A.T. 7 | Corsair 1300 | EKWB Loop