Very strange indeed.
Are you testing in the OutputTest directory with only the supplied Main.jack and your Output.jack?
This has the look of an uninitialized variable problem or an 'if' or 'while' statement that is testing an integer value instead of a boolean. (That's a common problem for me since most languages treat value != 0 as true, but JackCompiler uses value == -1.)
If you want me to take a look at your code, feel free to email it to me. (I'll be on the road Friday and Saturday so my net access will be spotty on those days.)
--Mark