Does the two-fingered secondary click not work in Windows8.1/Bootcamp? I just setup a Windows 8.1 installation on my 2012 MacBook Air using Bootcamp (5.1.5640). I've noticed that the two-fingered secondary click doesn't appear to work even when configured via the Bootcamp Control Panel - however two-fingered secondary tap seems to do it. I've verified that the trackpad doesn't seem to have any hardware issues - the two-fingered click works just find in OSX.

Is this a known issue or have I set this up incorrectly?
I had similar trackpad issues using Windows on my 2012 Macbook Air and fixed it using 3rd party software called Trackpad++. Give it a try.