When I installed WinMx 3.1 I put it in its own folder WINMX3\ WINMX that left the existing WINMX (for 2.6) untouched, I still have both setup and runnable here.
I still have the last beta version setup too, so I can transfer server lists across.
I aggree its sneeky to install in the same default location, would have been far better to have made it programfiles\winmx3 .
Guss.