I had the same problem with my logitec extreme 3D but i have found a fix. I take no credit for this I just found it with a search.
Battlefield Bad Company 2 Reversed Yaw and Throttle Fix
In order to fix the reversed yaw and throttle, go into the “air.dbx” file located under “bfbc2/input/air.dbx”, in this file you need to alter two lines:
1. To do that first open “air.dbx” in wordpad.
2. Search for “IDA_Axis1X” and make sure it is under the field for “ConceptMoveFB”.
3. Now change the following line “<field name=”ScaleValue”>1</field>” to “<field name=”ScaleValue”>-1</field>”.
4. Search for “IDA_Axis1Y” and make sure it is under the field for “ConceptYaw”.
5. Now change the following line “<field name=”ScaleValue”>1</field>” to
“<field name=”ScaleValue”>-1</field>”.
BFBC2 is in My Documents folder.
The throttle fix is step 2 and 3, the yaw fix is step 4 and 5.
Make sure you have them bound to what you want before you go into the file and change it or you won't find them.
I hope this helps everyone, it worked great for me.