m4a files don't seek or resume playback due to the text stream embedded in within them. Since this is an Apple/iTunes feature, I don't see podcast producers dropping them, and the current hacks in Doggcatcher don't always work.
For a more permanent solution, could you implement a "hack" that extracts the audio stream from the file and plays that instead? Either upon download or on the fly (though upon download makes more sense). There's even mp4box builds for Android that you could use: http://gpac.wp.mines-telecom.fr/downloads/gpac-nightly-builds/
I went into a little more detail on the FAQ comments: http://www.doggcatcher.com/node/2632