Is the Flash file the result of you exporting an edit from Premiere Pro? If so, then export it again using a lossless .avi file (Windows) or a lossless .mov file (Mac) from Pr. For Windows, I recommend the Lagarith codec and for Mac, the Animation codec works well, as does the Photo JPEG codec (my new favorite Quicktime lossless codec). Once you have the lossless intermediate file, use Quicktime Pro to convert for Podcast.
You can export iPod-legal .mp4 files from Pr, but there are issues with the Baseline profile and keyframes using the MainConcept encoder that ships with Pr. Those issues may or may not affect your particular video.