Update: 9/24/13!
After several years of dealing with this issue. I have found the problem. Under the "Address Book", "Control" tab "Ignore" was enabled and these two new entries were put in. "*!*@*(ct) " and "*!*@*(t)". And the Channel and Ctcp was check marked. Why and how these entries are put in is beyond me. Again, this only happens once and a while. Only after a disconnect and reconnect. But not on every disconnect and reconnect. I have spoken to several other people that this has happened to also. It seems to just be a glitch within mIRC that happens some times.
