I know this is a pain on the iPod lockup problem.
This is how I handled it. (Past tense because I used this 'hack' and the problem went away after a few weeks.)
It seemed to only 'deep sleep' when I paused "bookmarkable" files. (ie Podcasts)
I made a Playlist with one short song inside.
When ever I was going to leave the iPod for a while, I would "Menu" out and find that "single song' playlist.
I would play that song and let the iPod go to sleep. It would play on out and go to sleep. But it would never "deep sleep' after I played the single song. AND all my bookmarks on the podcasts would still be there.