MySQL and Drupal - db updates rolling back on their own

I'm having some extreme frustration with a site I've just set up on linode. I'm running Ubuntu 10, PHP5, MySQL 5.1.41. Here's what is happening:

Any changes I make to Drupal configuration that goes in the system or variables table is rolling back 5-10 minutes later - on it's own. Other changes, like creating nodes, changing menus, etc - works fine. Everything is default, configuration wise, from simply apt-get installing. I did verify that autocommit is On in MySQL but beyond that I'm lost.

Any ideas?