'pop-up' swf's affecting embeded swf's

could anyone tell me if a ‘pop-up’ transparent swf file (the sort that annoyingly appears as a commercial on so many sites) can prevent a regular, embeded swf from displaying?

we’ve just finished a page containing an embeded swf to be used by another company, who use ‘pop-up’ swfs. when the popups appear, our swf disappears.

any help appreciated, and apologies if this topic has already been covered.