I had a mare who always seemed a little unreasonable (rear, bounce etc for no apparent reason) she was on what I thought was a simple diet, chaff, pellets, barley, pollard. I change her onto a natural diet (unprocesed food) from the advice of a friend and she changed into a completely different horse. So I totally believe that there are some feeds that horses react badly to.
If you've found that she reacts to lucerne, then leave it out of her diet. I have found that oaten hay works just as well at fattening them up and contrary to popular belief it doesn't heat them up.