1. What version of Windows, and is it an elevated console window?
2. This is something I have planned to fix eventually.

Thanks, I can confirm that I have the same problem with Console windows in XP. Thankfully this works in both Vista and Win7. I will investigate this for the next release. As for the Notepad++ issue, for me it only duplicates for 1 second, then everythign gets sorted out after 1-2 seconds. Is this case with you as well?

After doing some reading, it appears that Console windows in XP can't be hooked. You can still use the TitleBar Buttons with the Console windows though, which can provide the same functionality. Sorry for the bad news, but fortunately this has been corrected in Vista and Win7.

Yes 3.1.5 did work with console windows in XP. This was a technical decision on my part, let me explain my reasoning a bit (forgive me if it's too technical). In previous versions (3.1.5 and earlier) DisplayFusion used a global mouse hook to intercept all mouse activity and see if it needed to do anything. As you can imagine, it sometimes caused mouse lag and general system lag. Starting with version 3.1.6 I am no longer using a global mouse hook, instead I'm using the existing application hooks to process the window messages. However, in Windows XP the console windows are special (because they run as a system process) and aren't allowed to be hooked by anything, not even an elevated DisplayFusion. As a result middle-clicking doesn't work. Unfortunately this was a trade-off that had to be made in the name of performance. The old mouse hooks really dragged a system down, especially under high CPU load. The good news is that Windows Vista and 7 both allow hooking of all processes, including the console, so your problem is solved if you ever migrate to Windows 7. I know it's not excellent news, but at least there's some hope.