What merge does is it just concatenates all those JS files which is all fine and dandy when there're no JS errors, but may break many previously working script when not. Whenever there's syntax error or something like that, interpreter will stop further script processing.
Lets say you have 10 scripts. 9 of them works just fine, but 1 -- not so much. Lets say you merge those scripts and the bad one happens to be the first -- it pretty much means that 9 otherwise fine scripts will stop working as well. Ain't that great?
So find you broken script and fix it. Then merge everything again and you should be good.
Tanel Raja