I just ran in to a similar situation with WP 3.3.1, in which the front page settings mysteriously disappeared from the Settings>Reading page. I think what catalyzed the trouble was that I tried to set the front page & posts page to be the only 2 pages that existed. Then, I changed the title & slug for both pages. When I went back to re-setup the Reading options, the front page settings had disappeared.
I couldn’t figure out how to get the settings back gracefully. Destroying my database and re-configuring WordPress worked to get the settings page back to normal– not ideal, but not a big deal since I was just getting things set up.