Yes, a knock can be intermittent.... and thus a royal pain to diagnose.
Was the engine warm when you did that compression test? The only way to do a compression test with a cold engine is wet and that's note really the best indicator either. Did you do a wet and a dry test?
If you run the engine and the knock remains long enough pull the spark plug wires one at a time. When the knock goes away or fades significantly you'll know which cylinder is the problem, then you just have to diagnose the one.
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