Typically when timecodes do not match the movie there’s a problem with the frame rate setting.

Here’s one way to check:

  1. Open your movie with QuickTime Player.
  2. Select Window menu→Show Movie Inspector.
  3. You should see a line called “FPS”. That’s telling you your frame rate for the movie.
  4. Now go to InqScribe.
  5. Open your InqScribe file with the movie.
  6. Select Transcript menu→Transcript Settings…
  7. What is the Frame Rate set to? Does it match your movie’s settings?

If they don’t match, select a frame rate that matches.