hey,
i know the problem your talking about.... i like to call it first position syndrome and nearly all guitarists suffer from it whether they know it or not.
its to do with the way you learn the guitar when you first start to play. you form alot of bad habbits that you then modify to let you play better as you go along.... but you can see it with most guitarists and probably all electric guitarists. The easiest place to see it is when people go to play in the first position and suddenly their technique goes out the window their thumb comes up over the top of the fingerboard and their wrist gets stuck out or they place their palm against the back of the neck and basically technique goes to crap...
this is where most peoples pinkey problems comes from when you break it down. you may have really good shape and technique on the higher frets but your pinky just jumps off teh fingerboard and has to travell miles to get back and in guitar distance = time + energy
so the problem comes for most people from teh fact that you tell your brain to do two things that you want minimal movement and really efficient playing... but that its ok to flail about wildly (ie when you get to teh lower frets and usually just the first position cause thats where you started with a couple of chords)
basically the trick is like someone said there a few posts ago that you have to consciously tell youur pinky to behave.... really focus on playing things you know not just teh chromatic excersises. cause you can teach your pinkey to behave just in that excersice like teh way your hand behaves totally different in the first position, but it will still be leaping off teh board when you play other stuff... so practice minimum movement with everything you play... and start slow cause its difficult to do and requires alot of concentration and like anything feels awkward when you first try it

eventually it will become second nature...
hope this helps
Steve