I had the same problems and tried searching for a solution a lot. No one seemed to know what was happening.
Finally, I went into my installation and tried to see if there was ANYTHING not standard about how it was installed. I realized that I had a directory in my wordpress root directory that was chmoded to 777. It was leftover from the way I installed an earlier version of wordpress.
I have no idea why this would have an effect on the theme, but basically after I removed that leftover directory (it had been empty, btw), I stopped experiencing the strange "theme reverts to default" bug.
Additionally, I do have other directories in my root directory side-by-side with my wordpress installation (for example, a files directory for my own use, and directories I have for friends to see notes to themselves), but none of that causes this bug (or seems to conflict). It was only the directory that was chmodded to 777 that seemed to cause it to happen.
As a test, I would like to restore that 'wordpress' directory chmodded to -777 and see if the theme starts to revert back to the default theme or not.
If I do this, I'll blog about it on pennyhero.net and hopefully google will index it and it will help others.
If you help me spread the word, or if people with questions about what I did want to, I can be contacted at emily [at] pennyhero [do] net or at http://www.pennyhero.net through comments.