Hey how are you building your game for Windows tunepunk? Are you using Visual Studio or Intel XDK?
I started testing in Windows Phone today and surprise! I'm having problems with touch like you are. Not exactly like you describe but still, touch craps out. I tried building with VS and XDK and my game breaks with both methods
Android has an option called "Developer options."
In one of these options you can make a chart that appears on the screen when android it detects a touch.
You can check if windows phone has a similar option.
In my case, sometimes (I do not know the reason), with this test, android does not detect the touch and the graph not appear.
However, when I write a message and repeatedly striking the screen, never fails and always the graph is displayed.