Xbuntu / AMD
Short description of error
If you have the manipulator enabled and deselect all the bones in pose mode it doesn't disappear.
Exact steps for others to reproduce the error
Create an armature
Go to pose mode
Enable the manipulator (by being forced to press "T" for the tools menu and selecting "Transform")
Select a bone
Press Alt+A to deselect all
...the manipulator stays there...