First click doesn't register?
In this case, it was caused by Spotify. It may have something to do with the ads that refresh every 10 seconds, but it started happening immediately after I opened it a minute ago, the 3-month hiatus ended the day I reinstalled it, and it usually happens in about hour-long increments, about how long I usually have Spotify open. I'm now 100% sure of this, it directly correlates with when the app is open or closed. It's strange, though, the window I'm in doesn't appear to lose focus, and this even happens when clicking on something in Spotify, but Spotify is what's causing it beyond a doubt.