I have exactly the same problem and am at my wit's end trying to solve it! I have done everything, even taken it to be repaired, where they put in a new logic board. Nothing has helped!
For me, the issue mainly is that if I close the lid, or manually put it to sleep, Wire Tap Pro will not wake it. I have several radio shows scheduled to record, and Wire Tap works perfectly for that. But it has to be wake-able. I can leave the lid open and the screen sleeps just fine, but the light will not pulse, and I know it is not asleep, because I can hear the new mail sound while the screen is black. I have checked my preferences and all match my husband's MB, which DOES sleep with the lid open. I have shut down everything, even shut down the computer, restarted it and left it at the login screen. I have disconnected everything from it, have even taken it far enough away from the Airport so that I have no signal. The problem persists! I sure would love a resolution!