I also have the same problem, but I don't think it's mIRC, as several other programs do the same thing. Try typing in Notepad, Wordpad, MS Word, and other things. For me, the pointer is hidden while typing in those as well. (Yes, I did check to make sure that the option was UNCHECKED, and it was.)
I noticed that if you have your pointer somewhere off of the mIRC program window while you're typing, it will not be hidden.