A summary of the issue.

I do not see this issue on IE, Firefox, Safari browsers.
Steps to Reproduce
wagtail start myproject with old version of Wagtail, I am on 1.10.1Experiencing this as well on ChromeVersion 59.0.3071.115 (Official Build) (64-bit) and Ubuntu 17.04.
It's worth noting that the links on the main page (outside the explorer box) are clicked when attempting to click something on the box itself (acts like a z-index issue).
Thanks for reporting this. Could you validate if this problem still persists after clearing the browser cache?
We have tested the new explorer quite extensively and my only guess is that some of the static files are still being served from the browsers' cache.
Closing this.. stupid of me to report even before checking simple options.
PS: Clearing the browser cache solves this problem.
Most helpful comment
Thanks for reporting this. Could you validate if this problem still persists after clearing the browser cache?
We have tested the new explorer quite extensively and my only guess is that some of the static files are still being served from the browsers' cache.