It took two hours to end the game originally, and by that point everyone was just glad to have finished. Does Redshirts Deluxe, the new version of Redshirts, fix any of the stalemate issues experienced in the base game or is it still stuck in an endless loop of attempting to end the game? Is the new expansion worth getting to make the base game playable?
The new version clarified a lot of the rules, and by all accounts fixed a lot of problems with the game including removing "play anytime" from cards.
Depending on what was causing your stalemates, this may have fixed it.
The new version of the rules can be found here: http://boardgamegeek.com/filepage/84529/redshirts-deluxe-edition-rules
Reading this may tell you if your issues have been resolved.