HUGE BUG (I think) in the checkboxes element override with disabled elements. Happened in Date field's Granularity element (checkboxes for year, month, day etc). Fields with data can't change Granularity, so the full element is disabled, so all checkboxes are disabled. Value_is didn't like that and overwrote the elements wrongly.
There was a BIG BUG in 1.4. If you don't have 1.4, upgrading isn't necessary. If you do have 1.4, UPDATE NOW!
Bug in 1.4:
User roles will be emptied if a user saves their own profile. This is since 1.4 because it adds #disabled_options to checkboxes, which fails if those checkboxes (user roles!) are hidden for the active user.