Just takes some getting use to. If I am understanding you correctly you are just not used to the pentatonic scale where you use basically your pointer finger and pinky/ring finger for every string and it is throwing you off (: One reason why I would say the pentatonic scale might seem awkward when you are used to others (major) is because you are using the pinky a little more perhaps, or because you go straight from your pointer finger to your pinky finger. In a major scale, you put down your pointer finger, then another finger, before you put your pinky down, so there are two fingers already holding down the string and your pinky doesn't have to use so much strength. When doing the pentatonic, you go from your pointer finger to the pinky so fast that basically the pinky is holding down the string all on it's lonesome (: which may take some getting used to. Maybe I didn't explain this right but I've had a long day (:

It's all about getting your hand used to it

This post was edited by Molle_fkk on May 7 2010 02:09pm

In long run, its actually faster and easier allways to pick down-up-down-up. You dont need to "think" or "know" what is the direction for the picking when changing strings, because you allways pick down-up-down-up.
I find it a lot easier that way, all i have to know is "what was the last direction for my right hand." In higher tempos (~220bpm+) the benefit is radical.