I just ran into an interesting issue. I didn't see any other relevant forum posts related to SetPoint, so here it is:
I recently started using a Logitech MX Laser mouse. The default behavior in SetPoint (4.80.103) for the scroll button click is "Zoom". Problem is, this prevents Display Fusion's Middle-Click Window Moving from working (among other middle click functions, like Veency on the iPhone).

After messing with several of the default options in SetPoint, I was finally able to get middle click to work as it would without SetPoint installed, and everything's kosher.

So if you're having issues with this feature of DisplayFusion, definitely check this setting in Logitech's SetPoint software.

EDIT: This only seems to occur when SetPoint detects a MX Laser or MX Laser BT mouse. My G7 and MX Performance mice do not exhibit this behavior with SetPoint.

The same goes for ANY program that wants to redefine your mouse buttons. I had this issue with intellipoint software from microsoft, thankfully they let you redefine the middle click back to... middle click. I can't seem to find the corresponding mouse 4 and 5 buttons though.