I used to do the same thing i think you're talking about, is it the case of instead of rolling and smoothly connecting with the floor you kind of fall onto your shoulder and roll. I remember doing that and how much it hurt
instead of avoiding the side i kept doing that on i decided the only way i was going to get better is to roll on that side more.
Its hard to get the rythm right so that you dont fall and hurt your shoulder, the way my sensei taught me was pinky to the floor and roll onto your arm, try doing it slowly and try not to think too much whilst doing it. Eventually it will just come natural to you.
I remember at a seminar i went to a while ago, i was training with a big group and i was falling on my shoulder a lot, why, i cant remember. So one of the shodan (a lovely bloke) took me aside and said "here, just watch this guy", the guy was a green belt and he break falled perfectly, barely made a sound, then he said to me "whats this guy doing before the roll?" So i watched again, then i noticed he was taking just a few extra steps before rolling to get his balance and roll properly. I thanked the shodan then on my next turn i tried it and i rolled without hurting my shoulder at all, but not quite as good as the green belt, who funny enough was a brown belt in judo too hehe.
Just a bit more practise and i'll be that good