Hard to say what might be wrong. Maybe you should try out ukemi in suwariwaza, from a kneeling position. Such a low ukemi you should manage fine, even if there is something wrong with how you do it. You increase your comfort, and you might find what it is you do wrong.
When people hurt their shoulders in mae ukemi, it is my experience that they do not make a distinct curve with their forward arm, so the shoulder takes too much of the force. But I have no idea if that is the case with your ukemi.
Try suwariwaza, and when that feels good, do some standing ukemi from a very low position - taking as long a step forward as you can (your back foot not following the least), before you begin the roll.