There's a better way but it's a bit complex and involves registry editing. If you can't get into the Registry Editor by yourself, do what AngryPixel suggests.
Anyway, adapted slightly from
GTAForums.com -> Possible fix for USB gamepad problem
Open regedit and go to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Contro l\MediaProperties\PrivateProperties\Joystick\OEM\
You should see a long list of VID_0000&PID_0000 listings, now you need to go find which one of those is your device. In most cases it is obvious, there will be a + sign next to it with some more options, but if you see multiple ones you need to check it in Device Manager, just find the right device (Mine was under 'HID-compliant game controller'). In the details tab the option is Device instance ID, which will give you the relevant number.
Once you have it, pick buttons from the drop down menu, for me I have 12 buttons so it was numbered 0 to 11. Note that in the testing page it is numbered from 1, so take away one from those numbers, or any numbers printed on the buttons themselves.
The test page is useful to help you here, Control Panel -> Game Controllers -> Properties. Then look what button press corresponds to what number, and compare that to where you'd expect the button to be.
Then, go back to regedit, and take a note of the 'Attributes', which will be a hex string that identifies what button is what. For mine it was
02 80 00 00 09 00 -- 00
where the -- was counting up in hex from 01 for the button 0 to 0c for button 11.
From here, you'd do a simple swap. For me buttons three and one were upside down, so you'd set Button 0 (button one) to be 02 80 00 00 09 00 03 00 and Button 2 (button three) to be 02 80 00 00 09 00 01 00.
You might need to restart for it to take effect. But for me the greater issue is AC09 doesn't even notice my pad in the first place.