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.