I'm guessing it's a TC mis-match between the PR file and the SCC file, but I don't know enough about it to suggest a way forward. Are you aware that there is a closed captioning forum on the COW? You might try it if you're really tight for time.
Problem solved. Here's what I was told on creative cow:
Open your movie in QT Pro and check the Movie Properties window to see if there are more tracks than just a Video Track and a Sound Track. If there are, select them and delete them. Then save your movie and try it in Compressor again. I've seen where the movie contained an extra Timecode Track and it prevented Compressor from adding the captions.