OK so I figured it out.

1) Go to http://www.filefactory.com/file/agfgedg/n/XinputEmu3_0_zip

2) Dowload the files and put them all in the "binaries" folder of the game

3) edit xbox360cemu.ini to change right stick's config. There's a line

Right Analog X=6 #axis index; use - to invert; precede with 's' for a slider eg; s-1; 7 to disable
Right Analog Y=-3 #axis index; use - to invert; precede with 's' for a slider eg; s-1; 7 to disable

swap the numbers (X=6, Y=-3, use "-" to invert if necessasry ), just check what's working with ur gamepad. Had to try few configs by myself before it was ok.

test with XInputTest.exe. When axis are ok during the test it should be ok.

That's it! Works perfectly fine for me with my Logitech controller

There is a "reverse axis Y" button but that's only to look up and down..the problem is moving forward and back with the joystick. The keyboard works fine when you reverse the forward and back buttons but they stay the same on the joystick even when you change it.

YES! I'm using the basic Logitech joystick and everything else works except the up and down buttons are reversed and it won't let me change them (even selecting from the control screen putting forward as "down" and back as "up"). Anyone know what to do???