Okay I've always had this problem and now that I am taking lessons and trying to practice regularly I am noticing it more and more.
Is it a muscle training thing and you just have to get used to it?
I am playing my Ibanez rg and the opening riff to Iron Man. This is further up the neck than some of the other songs that I have been working on. I find I notice the pain most the higher up the neck that I go.
Or is it because my forearm and hand are making an L shape?
Your fretting hand? Try to bend your wrist as little as pollible. If necessary, raise the neck up a bit, especially in long practice sessions. Also, try not to squeeze the neck any more than is necessary. A heavy fretting hand will strain muscles and tendons, especially with barre chords.