I have heard of a similar situation! A 1 1/2 year old girl that my son (same age) plays with was recently on amoxicillin for ear infection. She would wake up at night screaming. She was diagnosed with night terrors due to the amoxicillin. She was taken off of it and given another medication; problem solved.
Incidentally, my son also had problems with amoxicillin. The first time he took it, in April, he started vomiting. On the advice of a nurse friend, we made sure he only took it on a full stomach. He finished out his supply with no more problems. Then in May it was prescribed for his second ear infection. We went on vacation. His fifth day on the amoxicillin he broke out in hives. We saw a dr. who stated it was the amox. and said we should take him off of it, which we did immediately. We were told the hives would go away in 3-4 days. However the hives did not go away; instead they got worse. Three days later we saw another dr. who confirmed it was the amox. and started our son on steroid treatment and antihistamine. Slowly the hives went away. Needless to say our son will not be taking amox. or any other form of penicillin ever again.
I would say trust your intuition on this and other issues you encounter as a parent. I am sure that is what led you to ask this question and I suspect you are right on target!