I found another aspect to this problem. First it only seems to affect the files that are downloaded via iTunes from the podcast feeds. For example the HQMP4 file I linked to above plays fine and weighs in at 754MB.
However the one iTunes downloaded via my podcast subscription does not playback properly and weighs in at 1.23GB. So I deleted that entry from my podcast. refreshed the feed in iTunes with the "option+click triangle" feature and re downloaded The talk on drawbridge and now it is 719.2MB.
It seems to me there are problems with the podcast feed. I had another issue for the feed for example. The recent going deep episode on Advanced CRT 1 of n actually downloaded an MP3 file no the HQMP4 video file it should have. I also had to delete that and re download.
So all in all I think you might want to look at how your iTunes feed is working. At least for the going deep HD MP4 podcast.