Wow! My current drupal project blew up in my face today.
I was looking at how the Administrator Menu I had installed was pushing some items down in my template. To make sure that the floating super menu was the one causing the issue I shut off the module. After saving the configuration in build/modules a whole bunch of modules were shut off.
Whaaaaaaaat!
I tried to re-enable the modules that had been turned off inadvertently, but every time I clicked save, anything I had checked off would not stay, and other modules that were still on were being turned off. "This thing is eating it's own modules.", I thought.