One of the issues is what assumptions are being made by both applications when working with source that do not have timecode. Media Composer did/does import with a timecode of 01:00:00:00 whereas an AMA link starts at 00:00:00:00 – then it is up to Pro Tools to make some assumption as to what the timecode might be, etc. So all applications have to be on the same page when making these assumptions – we all know the saying of that goes with “assume”…
That being said, in future workflows, you might consider passing the WAV files through Sound Device’s Wave Agent where you can apply a timecode that gets embedded into the BWF chunk that is now used by all applications.
Secondly, you can do as Shane suggested and pass of the Avid MediaFile audio files with an AAF as it will contain whatever timecode and offset management as part of the workflow.
Thirdly, export all your WAV imports as BWF which will embed the timecode as seen in the START column and use those as new BWF masters in Pro Tools, but this does not gain you much compared to method #2 unless going to some program that does not supprot .mxf and AAF.
Michael