Hey guys, any ideas why this is happening? I play black metal, so lots of tremolo picking around 7th fret or so, however I play a lot of atmospheric BM as well, which requires playing on about the first 3 frets.

When I play down low for an extended period of time... (Fret 1-3) I get a burning pain in my shoulder. This only lasts for seconds literally, so it doesn't really bother me much.

In fact, the only reason it concerns me, is I don't want it to prevent me from playing in the future. Any ideas?
RIP Terje (Valfar) Bakken
Your shoulder should not be hurting. If it's your right shoulder that hurts, your picking technique is doing something very wrong. Picking comes from the wrist, not the forearm or upper arm.
Try adjusting your strap senor. A lot of the times a little heightening can make a world of difference in the realm of comfort/ease of playing.
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It's the fretting shoulder, and I'm not using a strap. I play classical style, with guitar on my left thigh, instead of my right... because I used to get wrist pain, but I started playing with the neck steeper and that helped.

No clue why shoulder is hurting.
RIP Terje (Valfar) Bakken
So you use a foot stool? I'll assume you do, if not then that's my suggestion.

Then, try to just sit with the guitar with your back and neck straight and relax as much as possible, especially from the shoulders and get used to that for a couple of minutes. Keep your fretting hand hanging relaxed on the left. Then slowly, while relaxing lift it up and concentrate on relaxing the left shoulder while the fretting hand goes to it's place. Then just keep that relaxation while playing. Always. If you have to, slow your playing down to as little as necessary to play relaxed.

You can always be more relaxed than you are without losing control of the guitar. Even if you know to relax while playing, that "exercise" is good to do often.
Yeah, when you're down at the low frets for a long time, it can be difficult to find a comfortable position. I just try and shimmy the guitar a little so I can reach it more easily.
If you are reasonably relaxed and the pain occurs its pathologic and you should see an orthopedist to be shure you are not accelerating a degenerative process.