If there's anyone else out there looking for help with this, I found a workaround: Disable Mouse Acceleration.
You can run the following command in the terminal, log out and back in (or reboot) and mouse acceleration will be disabled.
defaults write .GlobalPreferences com.apple.mouse.scaling -1
To put it back you can go to the Mouse settings and adjust the Tracking speed (just clicking on the current value seems to work). An alternate method to restore is to get the value of the original setting before you change it to -1 with the following command:
defaults read .GlobalPreferences com.apple.mouse.scaling
And then put it back when you are done, this requires you to log out and back in again (or reboot, if you so choose).
Your mouse will feel really different in this mode, but at least you won't click though windows anymore.
