How to? Inadvertent keystrokes?

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I have a long-running BTM file (it monitors a process). I keep it restored so I can see it. But with switching apps often, and with remote desktop sessions not always putting input focus where it's expected, some keystrokes inadvertently wind up in the console of the BTM file and they will be processed when the BTM file exits. Is there a way to avoid this? ... say by not accepting keystrokes while the BTM is running, or by clearing the input buffer at BTM exit time? ... using built-in tools ... or possibly a plugin?