I've had to downgrade from Galileo to Ganymede in order to use the version of the FlexBuilder plugin that we are licensed for. Since the downgrade, I have several times accidentally dragged files or entire folders from one part of my project into another (or even into another project). I blamed this on fatfingers the first couple times, but I just now watched it do it to me on what I definitely know to have been a single left click on the folder that the file ended up moving to.
Does anybody know if this is a known issue with Ganymede?
Not that I know of.
Here are the known DnD (Drag and Drop) issues with the CommonNavigator in Eclipse 3.4.x, none of them describing a scenario which would be close of what you are experiencing.