So I've done some further testing - I grabbed a closed caption file from another project, dropped it in and it worked fine. The difference between the two files, as far as I can tell, is that the one that works begins at 00:00:00:00 and the one that doesn't begins at 00:59:48:00.
I did read that in some versions of FCP at least, your timecode had to begin at 00:00:00:00. Ok, I used the Windows-based SCCTools command line tools to globally change the start timecode of the SCC file to begin at 00:00:00:00, and I cut the timeline to match that start point. Now they should be aligned.
When I try to edit to tape with this new file, it crashes again.
So this tells me there may be something else wrong with this file, perhaps Apple didn't fully fix whatever it was they said they fixed in version 7.0.3. Does anyone have any idea what that fix may have been? If I know what to ask for, I can have the caption service render out new files for me that will work.