Not sure, how hard are you pressing on the fretboard? I've read around here that your thumb should just kinda be there on the back of the neck. I have trouble keeping it in that middle or lower position on the neck, but I work on it all the time when I find myself not doing it right.
Does the pain come when you're playing frets 1-5?? That's a wide stretch to make comfortably, and I don't care if its wrong I used 1 & 4 to fret 1 & 3
Sometimes it works, sometimes I have to get used to the stretch.
Overall though playing efficiency comes from the left hand technique. Make sure you've got a comfortable bend in the wrist and are playing with the tips of your fingers.
