Pro Tools 11 and 12 include a feature called Dynamic Plugin Processing, which disables plug-ins whenever there is not an active audio region on the track.
This can cause synchronization problems with Auto-Tune in Graphic mode, since there is no way for Auto-Tune to keep track of the Pro Tools timeline when it has been turned off by Pro Tools.
Similar problems can occur when using Offline Bounce, Commit, and Track Freeze, even when Dynamic Plugin Processing is off.
There are two possible solutions to this problem:
Turn off Dynamic Plugin Processing by going to the Setup menu and chooing Playback Engine.
Avoid using Offline Bounce, Commit, and Track Freeze with Auto-Tune in Graphic Mode.
Consolidate all audio regions to eliminate gaps on any tracks on which you're using Auto-Tune in Graphic Mode.
Select all the audio on the track, go to the Edit menu and choose Consolidate Clip.