I have also had significant problems with re-descending, especially if it's the second or third dive of the day, or we have spent a lot of time wandering up and down in the shallows. (I've had to get out of the pool while teaching, because I simply couldn't equalize any more.). I think, even when we equalize early and often, there is still minor barotrauma that occurs and can be cumulative over a dive or dives.
When diving in shallow water and you are changing depths in a days time can definetly have an effect on your ears like barotrauma. I believe it is due to the fact that since we do not hold our breath and are more relaxed our ears do not equalize the same as a free diver would. Which is why it is best to try to minimize the varying up and down type of diving. This creates stress on the ears which can eventually lead to barotrauma injury. It is a good thing to remember when scuba diving in shallow water. Best thing is to stay at certain depth an avoid going up and down as much as possible, IMO.