When I export to swf, the floating controller for one of the mp4 is huge, no matter if I change the pdf options settings to 1/5x; it still comes out huge. Also, the mp4 stops playing on page turn. Should I postprocess these in another adobe program such as flash? or is there a way to make these adjustments in indesign?
PDF options won't affect a SWF file exported from InDesign. There are no controls I know of to set the size of the controller in InDesign or to set whether a movie stops playing on page turn for a SWF file.
I'm not an expert on video in Flash Professional so you may have to ask that in the Flash Professional forum.