Hey jkeith!
I know exactly what you're talking about, its a common issue when trying to develop
alternate picking speed.
Have you started your metronome speed really slow, then attempted to increase it over time? To get your muscles used to such intensive, focused action, you probably need to keep doing those exercises at a really slow speed (like 8th notes at 60 bpm, for example) and after about a week of practicing between 30 minutes to an hour (or longer), push it up a few bpm the next week or few days, and so on...
You'll probably notice that after you reach something like 16th notes at 120 bpm or something in that range, your picking hand is alot steadier and your fingers fret with alot more accuracy and clarity. You will, of course, want to practice alot of other exercises with this to increase dexterity, independance, and other techniques besides just picking (legato playing, sweeping, chords--probably the most ignored technique--,
string skipping, etc.)
The best way to learn techniques is also to learn to play a piece. Not necessarily a rock/shred piece, mind you, but a jazz or classical piece arranged for guitar would probably help more, as its not as "instinctive," so you'll have to push your technique farther and develop more.
Good luck man, and if I didn't answer your question... you get a full refund! LOL
K