I started having the same issue 2 nights ago...been using ST3 with the Air Turn pedal for a long time with no issues...all of the sudden at a gig 2 nights ago, every song was starting 2-3 seconds late...I made no changes to start/stop times in the sings, did nothing as far as options in ST3, etc. It's very annoying with another gig coming up shortly.
Oh, and I stopped using Air Turn midway thru the set and started selecting songs on my iPad manually with the same problem, that is, songs starting 2-3 seconds into it.