There are four possible reasons why the "Save Subtitled QuickTime Movie..." menu item would be disabled:

1. Demo Mode -- If you're running in demo mode without a valid registered license or an evaluation license, then the Save Subtitled QuickTime Movie is disabled.  Please request an evaluation license here: http://www.inqscribe.com/eval.html
2. Expired Evaluation License -- If your evaluation license is expired, saving is also disabled.  Please request an evaluation license here: http://www.inqscribe.com/eval.html
3. No QuickTime -- If you don't have QuickTime installed on your machine, it is not possible to save a Subtitled QuickTime movie.  Subtitles require QuickTime 7 (not QuickTime X). Please install QuickTime 7*  See http://support.inqscribe.com/knowledgebase/articles/15929-where-can-i-download-quicktime-for-free 
   *NOTE: Due to security risks, we do not recommend QuickTime for Windows users (more on this subject here).
   
4. No Media -- If you have a transcript open, but no media (e.g. movie or audio) open, then you will not be able to save a subtitled movie.  Just add the media to the transcript via the Media->Select Media Source... menu item.
5. .wmv media on Windows -- If your original media is a .wmv file, then you will not be able to save a subtitled quicktime movie.  Please convert your media to something that QuickTime can work with.  http://support.inqscribe.com/knowledgebase/articles/171152-how-can-i-convert-my-wmv-to-mov-
6. InqScribe 2.5 Beta-- The 2.5 beta does not use QuickTime, and thus no longer offers this feature. More information here.