Here's a very quick app I threw together that anyone with this issue can try out. (Requires Java)
All it does is print out the incoming mouse clicks, done in a similar way that I'm handling them in MewnBase for gameplay stuff. Would be curious to know if it works/doesn't work - and whether they seem mapped correctly for you.
https://drive.google.com/file/d/0B5QWRGJ_8C5rY2pMN1hrYXBhUkE/view?usp=sharing