Please check with the default MouseDemo example first. This will tell us whether the problem is from the FX3 firmware. Does the default mouse demo work fine on your Linux machine?
I tried the default MouseDemo too. Unfortunately, in Linux this did not work either.
Is it working for you in Linux?
I see there a 'mouseX' entry getting created under /dev/input/ for each new USB mouse. Unfortunately, for CX3 setup, it did not create such an entry in Linux.
We tried in Ubuntu 14.04 and 16.04 both.