I also had a problem similar to those experienced by many here: when Downloads Manager was initialized, the drop-down menus in the main navigation bar of my theme stopped working. I attempted to use the solution I found here: disabling Bootstrap js with
Downloads->Settings->Basic->Misc Settings->Twitter Bootstrap
Nothing seemed to happen. When I noticed that there was no confirmation of any kind, I switched from Safari to Chrome. I was able to change the settings (there was a confirmation) and the menus now work fine.
FYI – there is an issue with some of the admin controls in Safari (on a Mac running 10.8.5.)
