Using the latest windows release (0.9.6 pre-release) it's impossible to transpose. Having selected the notes to transpose if you use menu option "Notes - Transpose" a completely redesigned dialog pops up which looks like it should offer lots more options than the old dialog. Sadly it is impossible to use. I found the following problems:
1) Initially mpossible to use any of the drop down list boxes. However if you click on them several times they eventually come to life and provide the drop down list. However, no matter what you select you always end up with the default!
2) Under "transpose key" the radio buttons always show both the last two buttons pressed.
3) Clicking on the Transpose by Interval tick box has no effect (it's necessary to click the "up" radio buttion underneath)
4) The radio buttons under "transpose by Interval" will both be selected for ever once they have both been clicked.
5) The tick boxes for the options become ticked or not after clicking on them in a random way that is hard to describe.
Apart from this it looks good! Can't wait for it to work.