Autohotkey - Conditions under which it stops working?

I'm using AutoHotKey with the pre-made broadcast script (http://www.botbh.com/files/wow-bcast.ahk) with a same box Paladin/Hunter combo. I've already figured out that if I mess with the display resolution settings it will stop working. Sometimes, though, it will just stop working for no reason, usually at the worst time lol. What I have been doing is leaving the autohotkey CPU affinity for all 4 cores of my box, and then setting each Wow instance to use 2 different cores (i.e. Wow1 = 0 + 1, Wow2 = 2 + 3), and while that seems to make it more stable, on occasion it will stop passing key strokes. If I reload the script, it works fine again, but it is a bit annoying to have it happen when I desperately need to have strong control over the chars (like in a tough instance).

Does anyone know the conditions, other than changing display settings, that might cause it to stop passing keystrokes? I'd like to stop doing whatever it is that is making that happen :D.