Log keeps showing "Running application query took a while"

Is this normal? Or am I having some kind of issue with KM?

Sadly, yes. It is just Keyboard Maestro complaining pointlessly that some absolutely trivial request which should take a few microseconds is inexplicably take several milliseconds or more. But those wont generally affect you.

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Ok great. As long as this is not something affecting the performance, that's ok.
Thank you for clarifying