probably rotator cuff. it happened to me 3/4ths into my 1st cycle, but it was from shoulder press, but i can still feel it a bit w/ the up right rows. i stopped working my shoulders for almost 5 months. it got better, it just takes resting so the shoulder can heal itself. i dont know how bad yours is, but i'd avoid up right rows for now.
if its muscle pain....its not the juice. if its the tendons, or bursa sack, i would wonder. try a search on it. i came across something talking about how it can cause the body to not strengthen or replenish needed nutrition to the tendons/cartlidge. it could've been here or on another board. however, i dont how credible it is. good luck w/ your cycle and shoulder.