I have got to the bottom of this problem. Anyone using a Hotas Cougar who is having difficulty positioning the mouse cursor in AH read on :-
The problem with the MOUSEXY (x,y) command in Vista x64 anyway
The desktop result depends on the 'Pointer Speed' and 'Enhance precision' settings in Control Panel/Mouse. I finally got the cursor to the middle using 800,600 by turning off "Enhance" and setting Speed to the 3rd position from Slow.
However, in Aces High this setting failed miserably. The assumptiom must be that AH has it's own mouse control that over-rides Windows.
Oddly, the problem with loss of cursor positioning whilst playing AH seems to have been solved by using the Center pointer speed setting in Windows.
Conclusion :-
The MOUSEXY command can be made to work in Vista x64 but not by using the Foxy wizard because the wizard gives only the position of the cursor relative to screen definition.
The co-ordinates X,Y in the MOUSEXY command do not, unless you are lucky, refer to actual screen co-ordinates except proportionately. e.g. you may need 400, 300 instead of 800,600 to center on a 1600x1200 screen.
If you want to position within a game you may have to work your way to the correct position starting with something like 133,100. Maybe playing around with Cursor speed in AH would help too.