Bah it's not like every other DAW doesn't have it's own little issues. I use Pro Tools mainly because I roll to two or three different studios to work, and FUCK if I'm going to convert to some other DAW every damn time I need to work elsewhere. I've also had similar problems of bouncing individual tracks out of logic where they end up a few samples off of where they should be when using third party plugins - inexplicably.
Although I would think that if it's some Pro Tools and ADC/ buffer issue, wouldn't the whole track be off by a certain amount? So you could print it and nudge around?
I've just been using Massey DRT to print audio clicks and triggering off of those instead of midi. It's not as easy to adjust velocity, but it works.