Hmm, I fired up the gamepad control capx and set it to chrome. I didn't see any problems. As soon as I hit the "A" button, it registers right away. I tried previewing it maybe 6 times and never needed to reboot chrome. I never closed chrome in between previews (I closed the tab sometimes and didn't close it others).
I "think" my chrome browser is up to date. It says Version 43.0.2357.124 m
I am using an Xbox One controller, though it still says xbox 360 controller in the game text.