Quicktime Pro captions and converting to .FLV

Newbie here with a question about converting a Quicktime movie with captions added through a transcribed .qt.txt file. How can I convert this captioned movie to a .FLV file and still maintain the captioning? I do have an option in QT Pro to export as an FLV, and when I tested this on a 5 second clip it seemed to work well. However, when I tried to do the whole clip (15MB and 41 seconds), my computer completely stalls out and QT doesn't respond. Am on a MB Pro running 10.5.8 with 2GB of memory.

So, what options do I have to convert a QT file with captions to an FLV file - and still have the captioning available in the FLV file? Any help would be hugely appreciated.