Whenever im playing power chords alot, my thumb muscle gets tired from pushing on the back of the neck. If im playing barr chords its fine cuz I can just squeeze the neck. Am i doing something wrong or is this something that just takes time to build strength? When i first started learning i played alot in drop D so it was mostly barr chords. I know this is something i have to fix asap so lately ive been playing everything in standard.
I had the same problem. The way I pushed my thumb against the neck ended up hurting it. But I think its just a strength thing. I got used to it and I don't experience the soreness anymore.

-- Do as I say, not as I do. --
I'm actually a pretty seasoned player and i have this problem on occasion... *awaits a better answer*
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Action could be too high forcing your fingers to press harder and your thumb to press hard against the back of the neck?
My quick and easy fix to this is to do thumb-over powerchords. It probably isn't the best technique, but I don't use it consistently so it doesn't worry me too much.