…  have tried changing the simple edit shortcuts, but to no avail …

The metatools for transposition are in the Selection Tool, not in the Simple Entry Tool.

From your description it sounds like you will have to program the {Transpose Down} metatool again.

To do so, press Ctrl+Shift and a number key (6-9). Finale displays the Transposition dialog box.

In the Transposition dialog, set the transposition you want to program, and click OK.

Thanks for your help it has pointed me in the right direction. If I press cntrl+ shift+a number I get the box for transposition. As expected cntrl+shift+8 gives me transpose down
However there seems to be no shortcut key assigned to this function. cntrl+6 works so does
cntrl+7. However cntrl+8 & 9 do not work.

I have worked round it by using the TG tools plugin. Using that I have assigned cntrl+8 to transpose down. This brings up the box and I have to press OK to get the transposition. An extra keystroke....a bit better. 

Thanks