Hmmm that sounds like its reading constantly a value from the controller sticks. If you connect a controller in to the computer while holding into a certain direction, that becomes the "default direction" and it will constantly keep reading a wrong value. Disconnecting and reconnecting the controller will fix this. Rebooting your computer while making sure the stick isn't held into any direction will as well fix this.
I did test my own 360 controller and it should work fine as is so it shouldn't be an issue with the controller type.
If nothing does work it sounds either like the controller itself is configured poorly (bad drivers or such) or there is an issue with a deadzone, in other words, the stick on your controller is a bit loose and the game detects it as an input. Not sure can you configure deadzones on our engine in any way as it is right now . .
Try to disconnect the controller and put it back in. Also, you can just disconnect the controller and map in the buttons with your keyboard so you can at least play with keyboard if the issue cannot be solved easily.
Also, if you open MM25DConfig.xml with a Notepad, there is a section like this :
-<Controls>
-<Mapping>
-<ArrayOfAnyType>
Under there you do see your controller inputs if you feel like entering them manually though that's rather difficult to do so I wouldn't recommend that if you don't feel experimental.