Well, there is a difference btwn pain that is associated with acute tendon damage and the momentary flash of pain in, say, nikkyo, that is the result of momentary touching of the nerve rich covering of 2 bones; it hurts and is gone. HOWEVER, it the lock is applied correctly, so that uke is actually locked up all the way up the arm, through the shoulder, to his center, then the pain will only flash on if and when uke turns to regain his balance.
A good sankyo lock has my balance from the start; if the person starts whipping me around using pain compliance to make me follow him or dance around, to me that is gratuitous; he could have just dropped me from the start.
Pain compliance all the way down to me indicates the person doesn't actually have me locked; I'll move and I'll tap but I'll also tell him it was purely pain, please try again.
My two cents
Since you move and tap, I'd say the person has got you locked pretty well, since you can't do anything.
Of course, in the ideal situation you have a combination of pain compliance and taking uke's balance, but in certain cases, you only need one of the two.