Have you had anyone look at your positioning or video your positioning when doing theses movements?
Video is helpful because you can see exactly what you are doing vs what it feel like you are doing.
There could be smaller deviations in your positioning which are contributing to the pain.
You can identify if there are any changes in your positioning throughout the movements.

Your shoulders may have been tired from the 1st wod which may have impacted your active shoulder position for the 2nd wod. Are your elbows in close to your body when doing pushups?
If your elbows are away from your body this internally rotates the shoulder which is not a good position.
Nate Helming has a good video that goes through positioning and transfer
 http://www.youtube.com/watch?feature=player_embedded&v=Rr9pVMcldgU