I have the same problem, and I've had it for a long time. For a period right after installing macOS Sierra the problem went away completely, but it has come back over the last months or so and seems worse than ever (when I installed Sierra a completely fresh install, manually copying files over and re-configuring all apps).
My "e" key is constantly partly working, sometimes it will register the hit but I estimate than more than half the time it doesn't and it's slowing my typing down so hard that I can barely focus on working.
Other keys such as "p", "ENTER" stops working randomly for a period of 1 to 10 mins where I can maybe sneak a "p" out if I insist and keep hitting the key and then later on "p" works constantly. "e" is on the other hand constantly unstable but it didn't use the be like that even when I had the problem prior to Sierra. Back then it was only "p" and other keys that was creating problems randomly.
I have done extensive "research" on this keyboard issue over more than a year and have never found any solution. I've reset "pram" and done pretty much anything possible I could think of or found in other threads around the web. Accessibility features are disabled and playing around with the settings does not change anything.
Did anybody make any kind of progress on this issue? I am considering to do a fresh re-install, but being a power user and developer, a re-install is days of setting up apps and dev tools and I'm not sure it will help anything.