Have you had them looked at by an orthopedic or sports med doc? There are a couple of things that are pretty easy to fix possibly without surgery that might be going on. There's a little tiny muscle that goes through your shoulder from the humerus to the underside of the scapula (shoulder blade) that can get pinched, especially if the bone where it attaches on your arm has a hook shape to it. If you get any inflammation in the joint (and it sounds like you have), the little guy (supraspinatus) can get really jammed up. Decreasing the inflammation in the joint either with meds or a cortisone shot really helps. Sometimes they have to go in and file down that little hook shaped acromion to give the muscle more movement space, but not often.
Another issue can be a muscle imbalance in the groups that stabilize the shoulders. There's another small muscle group that we don't use very often - the serratus - that helps stabilize the joint in certain directions, some of which we encounter when taking falls or rolls. If that group is a little weaker than the other groups in the area (pecs, delts, traps, etc), then the force of the fall plus the stronger pull of the bigger groups can allow the head of the humerus to shove up into the joint, smashing the heck out of the bursa. The result is a nasty case of bursitis, which then gets worse every time it twinges (like when you roll over on it in bed). A physical therapist can test the muscle group strength, and give you some really odd looking exercises to help.
I had a combination of both issues in my shoulders, and have dealt with it for almost a year now. Three months ago I got the cortisone shot in my left shoulder, which is much better. It's still easy to jam it if I fall wrong, but it doesn't stay that way. Hurt for a day or so afterward, but part of the reason was that I had to go back to work right after the shot (and was doing something where that arm couldn't move much for the next 4 hours). I need to find a time to get the right one done.
I did take some time off from taking the ukemi that irritated it (kaiten nage and ikkyo were the worst), and did weenie sit-out falls on some others (like kote gaeshi). It helps I'm also practicing in a different dojo doing a completely different style of aikido too, having gone from an independent dojo with an almost hapkido/shotokan flavor to a Ki Federation group. My new sensei has also changed the way I do rolls (and the way I sit, stand, walk, breathe, etc....running joke with him) and they have become much more comfortable. As they've gotten better, I've relaxed more, and I definitely don't get hurt as often when I am relaxed.
Good luck, and be patient! Shoulders take a long time to heal.