I can't think of why.
I think you're code (posted here at least) isn't right for the javascript window:

scrollbars=javascript:launchwin('map/map.html' , 'newwindow' , 'height=150,width=300");

shouldn't scrollbars = "yes" or "no"?

Could you (as a quick fix!) call the javascript window from the root somehow rather than in the MC?