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:
https://support.apple.com/kb/DL762?viewlocale=en_US&locale=en_US

More about this issue here: 
http://blogs.inquirium.net/inqscribe/2012/07/bugs-in-quicktime-7-7-2-for-windows/

-- 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).