Does the same behavior occur if you Export a MOV or AVI from Flash itself which you could import into Premiere?
No, but I was having issues with exporting the animation under those extensions. It turns out that when Flash exports as .mov it basically records the playback within the program, so I'd end up with a bunch of missing frames whenever a complicated part of the animation caused Flash to slow down. I was able to get around this by lowering my animation framerate both in the project and in the export settings. The result then contained all the frames and was easily sped back up in premiere to play at the intended speed. As far as my original question I found an old thread which basically asked the same thing, and the answer was no. There is no way to change the way Premiere handles .swf files without altering your animation.
I am no Flash expert but recently used some Flash animation (swf) supplied from elsewhere successfuly in a PPRO project.
Cant you just use a flattened flash file?
Maybe you can export separate layers from Flash if need be?
FWIW: I had no issues opening swf in PPRO or AEFX.