JSFL: Change Output name in Publish settings

We are getting weird mask issues in swfs when we export a swf movie. But this doesn't occur when publishing the swf instead. 

Because we need to publish layers of the doc as separate swfs, we can create code to go through the layers and turn each one on at a time before publishing the doc. But this doesn't work because it saves the swf as the name of the doc each time as set in the publish settings "Output name". So... is there any way to set the output name in between publishing?