When you use Pro Tools to import raw production source audio that was not exported from an Avid video editing application—such as audio delivered separately from an AAF or OMF sequence—that audio may be offset with the audio in the AAF or OMF sequence by as much as half a frame.
This misalignment results from the incompatibility between frame-accurate time stamping in Avid video editing applications and sample-accurate time stamping in Pro Tools. When you attempt to link the two, the misalignment results.
In order to repair this discrepancy, you may need to offset the raw production source audio after importing it into Pro Tools, either manually, or with a utility like SynchroArts Titan.