Well if it's in the same folder that might be your issue Mine are on the same drive, but different folders.
Its for organization's sake.
C Drive - 80 gb OS partrition + important document
G Drive - 150gb Games partrition + Modding tools and setup
E Drive - 250gb I have no idea what to do with this one 
D Drive - 100gb A second OS which I rotate from server08x64 to ubuntu
F Drive -115gb No idea what to do with it
H Drive - 225gb Again, no idea what to do with it
Sub Folders of G drive: Games, Modding, Downloads, Programfiles
Games folder subfolders: Stardock Games, Halo, THQ, Stardock (impulse)
And so I have both versions inside the Stardock Games folder. I also like to rename everything, maybe that made impulse confused as to which one it should update. 