@peternlewis You are correct in your understanding of my description. The missing keystrokes continue to happen, though sometimes the problem is much less severe than at others, and it does seem less so lately.
The accent popover and missing stroke can happen anywhere I'm typing.
My goal at this point is simply to add information to this thread as it occurs, an evidence trail so to speak, that may eventually lead to a solution.
I do continue to suspect that Keyboard Maestro is at least involved in the issue (not saying it's the cause), because the issue always seems to completely resolve immediately after quitting the Keyboard Maestro engine.
An additional bit of information: I have noticed that the "Cancel All Macros" submenu (under the Keyboard Maestro menubar icon) blinks sporadically.
Here is a dropbox link to the a screen video of the phenomenon occurring: (Caveat: I think the software I'm using to make the video (SnagIt) is, itself, causing the submenu to blink once a second, so this video is only intended to demonstrate the blink event, not the frequency of the blink.)
Video of "Cancel All Macros" blinking.
When not screenshotting the submenu, the blinking continues, but only (usually) sporadically, as in once or twice every several seconds. Other times, it will blink once a second, without SnagIt's "help."
Also, I looked at the engine.log. I'm getting a "ton" (15 to 20 within a second) of...
"Invalid Plug In Action with Name Execute a Script in Terminal"
...and...
"Invalid Plug In Action with Name Get Finder Path."
However, I do not see additional entries (those listed just above or others) in the engine.log timed to each blink.
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I see the blinking submenu is described here as well: