I am experiencing the same issue. I have an aftermarket touchscreen from TOUCHKIT that is recognized by Windows 8 and i can calibrate it for tablet and then slide the apps screen left to right, but the flick and gestures do not work anywhere else and it gives the message "You cannot use a mouse to perform a flick". When i install the driver for the usb controller, the tablet choices disappear in control panel and then the touch screen only acts like a mouse would and I can no longer slide the apps left to right with a gesture. I refreshed Windows 8 and started from scratch with the same results.
I am tempted not to install the TOUCHKIT driver, but then I am not able to use some of the touch screen functionality.
Why cant I have the best of both worlds? A responsive touchscreen with the flicks and gestures.