Hi,
I suggest that you set up a personal configuration
for your controls , then define the rudder for your pedals
and exit the program.
Then find the CFS3 folder inside your Windows
folder (it should be someting like :
"C:\WINDOWS\User files\Microsoft\Combat Flight Simulator 3.0")
open the ...xca file with an editor and change the
value of that axis with an "-" , for example:
before :<Axis ID="Y" Action="Set_Yaw" Scale="64" Nullzone="36"/>
after :<Axis ID="Y" Action="Set_Yaw" Scale="-64" Nullzone="36"/>

it worked fine for me
have fun!