Well, I have this problem, well, it ain't really a problem, still...When playing fast or quite intensive (as somethimes occures to happen in a metal band ) after a while my rightunderarm (picking arm) starts to hurt and my fingers seem to go less fast, like they're slowed down by something. It starts mainly when playing the E string (lowest on my bass) so I figured it out that it had to do something with the position of my hand. Is it because my thumb is to close to the strings, or because of the fact that when attacking my fingers doesn't rest on the string below (as is with attacking the A-D or G strings)?
How long have you been playing, to me it sounds just like lack of sustain resulting in cramp? I've been experiencing picking hand pains in my wrist lately, tehres a post in this area that may have helping tips for you.