I'm getting the same trouble. I'm not 100% sure it's a false positive -- it's a big site and while I've gone through things as carefully as I can, I can't say for certain I've gotten everything.
However, one thing I noticed is that when I use the Chrome debugger on it, I get a JS syntax error when I do the manual scan. That is definitely ungood. All the bubbles in the "manual scan" area stay orange. The first time I ran it, it id'ed a couple of suspect code fragments that I was able to certify as being innocent. I'm guessing that there are others that are missed because the JS GUI is crashing before it gets to the point where it can show me them.
I'm running WP 3.2.1 and WPAV 1.1