The delay in the touchpad is irrelevant of application. The two finger scrolling issue seems to be application dependent. Right now, my surfaceforums.net thread will not two finger scroll in Chrome, however, my second tab (Reddit) scrolls perfectly fine.
With that said, I'm not too worried about the scrolling issue, but the touchpad "delay" is the annoyance. It's hard to reproduce too. For example, I just lightly scrolled around and it worked instantaneously. Then I just tried it again and it had a delay to start moving around.