I got a pair of S1 gloves two weeks ago and the lower right portion of my palm (where my thumb ends) aches after 10 minutes of riding.
The left and right gloves are pretty identical and my left hand is happy as a clam so I'm puzzled what's up. I've felt around in both to see if one had a hard part in that general area and didn't find anything, and they fit really well.
How much time do you have in them? Gloves will break in quite a bit.
I've had the same issue where one glove was too tight and the other was fine. You could always have a buddy with one size bigger hands wear the right one for a little bit. Brian has done that for me before.
I would say they're going to be getting there soon. I fought with my handroids for about 5 long rides. eventually i crammed markers in the pinky all day and then i won the battle.
some gloves comply within the first couple rides, some will take a few weeks. if you still have problems after another week i'd find a buddy with hands that are a size bigger than you and have him (hopefully not her) wear them for 20 minutes or so.