With Soundflower running, once I resume from suspend, Soundflower becomes unresponsive and my Mac audio has problems until I restart. The problem began with the recent OSX 10.8.5 update. I'm running Soundflower 1.6.6b.
CONFIRMED THAT THE LATEST 10.8.5 Update fixes this problem: OS X 10.8.5 (12F45)
I've just re-installed Soundflower to see if this is fixed. Apple specifically mentions this HDMI bug in their OS update.
After a full day of testing and putting the mac in/out of sleep mode, I've confirmed that SoundFlower is working again. . . for now. :)