It was the third fret, but only on strings 1,2 and 3. But I think I found the problem... And inadvertantly made it worse! LoL
Well, it seems that I had a loose fret and it wouldn't just simply "Tap" back in. It sprang back up every time I pushed it in and I didn't notice it. But every time I tapped it, I flattened, lengthened and bowed it more and more. Turns out when I started tapping them all in, I actually broke them free, that's why I was getting the problem up and down the neck. Now I've got a few dead notes.
I went to a music supply today and got a few lengths of fret wire and some epoxy. I plan on refretting this guitar little by little during the week. I figure I'll do a little sanding on the nut and the bridge to lower the action a bit too. Hopefully not too low though!