Happens to me sometimes, usually with Requests to you, Giz,hehe! :P I don't think this particular issue is about the amount of messages. I've noticed that I DON'T get ANY pop-up message about waiting Request before I visit the Alter of Love. So if I don't open it, I have no chance of knowing that anything was sent to me. Because of that I sometimes forget to accept my own Requests to the ponies on my second account, as I don't visit the Alter of Love on a daily basis there, like I do on my main account :P