Admin Menu at bottom of screen
Drupal core 7.16 with Omgea 7x-3.1 theme and loads of modules. Just experienced the similar behavior where admin menu was locked at bottom of the page. Read through this, decided to not touch Skinr and instead:

Home » Administration » Configuration » Administration

Turn of the "Adjust top margin", save, clear cache, turn on "Adjust top margin" AND "Keep menu at top of page" - this solved the problem in my case.