I've also had similar problems, usually whenever I try to stack a cluster (so far Omega Cent, Tuc47 and especially problematic The Jewel Box) I need to drop the threshold right down as Lewis suggested. At which point some of the other settings I usually select change eg "Use median combination method" to something else that I cannot recall right now and takes three times as long to process.
Still learning and bumbling through it all...
Having said that what a great feeling when you see that image peel back and you know you've got a winner!
