I did not answer your question because I do not know the answer to it. I would think it has something to do with the registry, but that part is heavily encrypted and I do not know much about it. Maybe it is a problem with IE's encrypting or maybe it is the registry not saving it.
Concerning IE and Chrome. I use them both. Sometimes IE works better, sometimes Chrome works better. Sometimes I have problems with IE, sometimes I have problems with Chrome. They seem about even to me.