Magic Trackpad 2 Foreground Window Focus Issue

I've been having the weirdest issue with my Magic Trackpad 2 on El Capitan (10.11.3.) When I'm in one app's window and tap/click to another app's window, the new app's window comes to the foreground but the old app is still in focus. So if I try a keyboard command at this point or type some text, it's actually performing that in the old app and not the new foreground app.

Say for example I have TextEdit and Safari open and I'm browsing a page in Safari. 50% of the time if I use my Magic Trackpad 2 to tap or click into the empty TextEdit document window from Safari, the TextEdit window will come into foreground focus and Safari will be the background window, but if I start typing text or hit CMD-N for a new document, it'll operate on Safari instead of TextEdit. This is just an example – it literally happens with any app.

I've messed with everything: accessibility settings for the Trackpad, trackpad settings, etc. No background apps or mouse extension apps installed. Tried both wirelessly and plugged in via Lightning cable. Magic Mouse doesn't seem to have this problem, Trackpad 2 only.

Anyone else having this issue? It's driving me crazy and makes using the Magic Trackpad 2 on OS X pretty useless.