An annoying bug: when you have JabRef open and then start TeXnicCenter and try to run your code with a reference to your JabRef-database, TeXnicCenter crashes. I did not find any solution for it, but at least it helps to first open TeXnicCenter and then open JabRef. Don’t ask me why, but it often helps.

According to the bug-report it has to do with the link to your bib-file: http://sourceforge.net/tracker/?func=detail&aid=3042060&group_id=36323&atid=416430

See also: http://www.latex-community.org/forum/viewtopic.php?f=31&t=371&p=1782