Bumping up an old thread, but I was having the same problem and have found a solution for it in case anyone is having the same problem.
My issue was with Diggnation HD as well, so YMMV with other podcasts, but I suspect the problem to be quite similar.
HD podcasts downloaded will work, but iTunes won't transfer the podcasts over due to iTunes being stringent on the typo of video it can transfer. Apparently, Diggnation HD was in a higher video profile than what the iPad officially supports (3.1), and hence you will need to change the video profile to 3.1 manually with a hex editor.
It's pretty straight forward, but one additional step would be to locate the podcast within iTunes (Cmd+R), delete the actual podcast from iTunes but keep the file, make the necessary hex changes to the podcast and then transfer it back to iTunes.
A bit more fuss than needed, but until podcasts provider change to a compatible video profile or Apple releases a software update (more for iTunes than the iPad) to fix this, this would at least get your HD podcasts playing.