QuickTime X for Lion is not a separate download. If it needs to be reinstalled, you'd have to reinstall Mac OS X. A could of things you can try, though:
- check for any third-party codecs or other plugins and either update or (preferably) delete them and see if that makes any difference
- run Activity Monitor, set it to show all processes, and see if there's anything that's popping up that's using a signficant amount of CPU time at the time these stalls happen
- try the movies with a different player such as VLC Media Player and see if similar stalls occur. If they do, then the probably is most likely with the movie files, not with QuickTime.
The above suggestions presume that these movies are local files, not something being streamed from another system or site.
Hope this helps.