There are a few bugs in QuickTime 7.7.2+ for Windows. If you aren't seeing any subtitles at all in your exported movie, you're probably experiencing this bug.
If you use Windows, you might want to uninstall QuickTime 7.7.2+ and download the QuickTime 7.6, which we've found to work best with InqScribe. You can download QuickTime 7.6 from Apple below:
More about this issue here:
-- Updated 2015
[The problem has not yet been fixed in newer versions of QuickTime 7.7.3 or 7.7.4]
NOTE: Due to security risks, we do not recommend any version of QuickTime for Windows users (more on this subject here).