I don't know the problem you are talking about, but I use a simple utility that allows you to create profiles and map the mouse buttons however you wish. I don't know if this would help with the issue you are having, but you could give it a shot.http://www.logigamer.com/
I use it with many games that don't recognize all the buttons on my MX500 and MX700. You can bind any key for any button, including the wheel button.
Hopefully that will help you out. If you have any questions about it let me know. I've been using it for awhile now without problems. Switching profiles is as simple as clicking it. It can even auto-detect what game is launching and switch to that profile, but I haven't had much luck with that yet. Make sure you get the full package. You need the full program to setup profiles, while you can use the Lite version to simply select profiles and use less memory.
Like I said, I haven't had any problems like your own, but I wanted to use all the buttons and this might be a good workaround for you as well.