I wouldn't even try setting intonation with a clip on. Use a tuner you plug into, if you can borrow one.
My Snark doesn't like picking up the 12th fret harmonic on the B string of my Stingray 5. It reads it, initially, but drops it, then doesn't register a tone at all.
One of these days I might actually read what I've typed, before I hit the post button.