If you're capturing (for example) your speakers of your mac via soundflower/wavtap, you need to make sure the volume for the speakers are all the way up before switching it to use soundflower/wavtap. The way to do this is by going to system preferences, then sound, then the output section of devices, then you select your speakers briefly, set the volume to 100% below that, then switch back to soundflower/wavtap.
I'm guessing that's the issue, though I could be wrong.