I know this topic is old now, but I still have some software that I have paid for that wont work, and there was nothing to mention it will not work if you have endpoint installed. Never had the problem with any other version of ad-aware, I don't really wont to delete one or the other, as they both see things the other does not so belt and braces and all that.
I was having this problem, and was talking to tech support by email, as soon as I mentioned that I had SEP installed on my machine, the replies stopped, and I have not heard anything since. I clean built my machine (yet again) and it works fine installed on it's own. I tried installing it before SEP, and after it, same effect, just waiting for scanner, then says finished, but has not scanned anything.