Whatever you're practicing with a metronome, break down the elements separately then put them together....if you're practicing some alternate picking runs and not keeping up time...play the left hand part to the lick first to the beat, then the picking part...then put them together....sometimes your hands are just out of sync but your picking is just fine....another OBVIOUS thing is be sure to come in directly on the click...sometimes you're coming in a bit late or early and you just feel forced because you didn't come in to the click on time.
Another thing is just the way you think about it...use the metronome to guide you but let the beat in your head/internal clock take precedent....just use the metronome to keep you in tempo/time....that can ease things up and not feel so stiff. Just keep doing it.