Typically when time codes 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 framerate that matches.