It sounds like you're using your hydrometer directly in your kettle or fermenter. I would suggest (if I'm correct) that you take a sample with your auto-siphon or wine thief and put it into a graduated cylinder. Then when you drop your hydrometer in, use paper towel to wipe away the bubbles. Also, make sure you are letting the wort get to 60F or so, otherwise your SG reading will be way off.
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