Is this good or bad? I notice that if I try doing fast licks across the neck I get these. Does it mean my muscles are getting stronger?
how long have you been playing? Are you playing standing up or sitting down? and which arm is hurting?
LTD EC-500 - 18v mod
Roland Cube 30
DigiTech RP-7 Valve Guitar Preamp/Multi-Effects Processor
generally speaking, NO pain is a good thing, usually means you are doing damage to yourself. Might want to go easy for a while until your arm stops hurting, else you might put yourself out of action for a lot longer.
As rich420 said, its probably because of you're posture. I can't really say what to change because I can't see you playing.
LTD EC-500 - 18v mod
Roland Cube 30
DigiTech RP-7 Valve Guitar Preamp/Multi-Effects Processor
Wank with your right from now on, ease the stress

Maybe its bad technique
2003 Music Man Axis Pacific Blue Burst
probably isn't but i got carpel tunnel in my left arm after 5 years of playing. I had surgery and now, 3 years later, i'm playing with no pain at all. It's worth getting checked out because i just though it was the muscle, boy was I wrong.
My left arm gets tired after fast continous licks, but never to the point of pain. just tired, so i take a break or do something at a slower pace then im fine.
Reinhardt 18 Head
H&K Tubemiester 18 head
Blue 6505+ head

TC Electronics G Major
MXR phase 90, Pigtronix Echolution 2
Digitech Whammy (5th gen)

ETB Infinity x2
ETB Yoda

That used to happen to me a lot playing thunderstruck but I kept going, I think it's just like lifting weights, you pull the muscle and it heals stronger. I used to only be able to play the hammer-on pull-off licks for a minute or so straight, but now i can do it endlessly.
Godin Freeway Classic
Ibanez Concord Acoustic
Roland Cube 30x
Zoom G2
just ease the arm and mabey ice it or don't push on the strings as hard. also try to straiten out ur thmb so that it is verticle 99.9% of the time.