Any submit in user settings seems to reset them. I tried ordering my nodes, then changed another user setting, and it was reset. After that I ordered them, and then hit the submit button without changing anything, with the same result.

Off-topic, one thing which might be nice as an option would be "treat front-page as any page" so that if you always want the same nodelets, the same order, etc on all pages, you don't have to set it twice (which can be difficult when the link or Perlmonks is being slow and you're adjusting nodelet order, which takes a number of page loads).