When configuring the mouse in the GUI installer, you can select MS Intellimouse (PS/2) which is a three button mouse, and the emulate 3 buttons is automatically selected. Deselect emulate 3 buttons and press next then go back to mouse configuration and emulate 3 buttons is again selected.
This bug is fixed in beta3.
*** Bug 10032 has been marked as a duplicate of this bug. ***
Appears to have resurfaced in 6.2
It has not quite resurfaced, that's why I openend a new bug, when you go back it does remember the state of the emulate 3 buttons box now, which was one of the 2 bugs reported here. The other bug, that it should not select emulate 3 buttons for an intelli mouse (wheel mouse) at all, is still open. The confusion here is that 2 bugs we're reported in one entry, hence the new entry.
The auto selecting of emulate 3 buttons for imps/2 is still there in 6.9.0 (winston beta1)
Seems fixed in 6.9 beta2.