Well when u setup the ps3 audio settings you have to check off which audio types ur receiver can play. There is Dolby 5.1, AAC, DTS 5.1, & the 2 I left unchecked were linear PCM audio.
Also, I noticed something strange. Right before the game loads, the screen flickers for the HDMI and then the receiver displays "Unlock"? Then my sub stops working. According to the sony receiver manual, "Unlock appears on the display if no digital signal is input through the optical jack.
I think this is the source of my problem but I can still hear sound through all the speakers, just no bass. I'm guessing that when the screen flickers for the HDMI it has no audio connection in that split second. This is tricking my reiever into thinking there is no Optical connection hooked up.