Long queries are not timing out properly with an alert box. They just apparently go on forever in the client, although they've really moved to processing in the back-end. Following the suggestion in this thread https://groups.google.com/forum/#!topic/i2b2-install-help/mzSI5hgeiO4 I was able to find the error:

js-i2b2/cells/CRC/CRC_ctrlr_QryStatus.js:570 Uncaught TypeError: Cannot read property 'firstChild' of undefined

The end_date is null. I worked around it by changing the line to:
var endDateResult = i2b2.h.XPath(temp, 'descendant-or-self::end_date');
if(endDateResult && endDateResult.length > 0)
     self.QI.end_date = endDateResult[0].firstChild.nodeValue; //Query Report BG

I would submit a patch but don't know enough about i2b2 to know if that's just a hack, if a null end_date is unexpected, or if you would rather apply a better check to all the query properties in that function.