I actually has this problem, and I checked to see if I by chance had checked that box in options. It seemed I didn't have, also as I remember I hadn't.
Anyway, apart from my bad grammar, I tried checking it, pressing ok, and saw the exact same behaviour, no difference. I then unchecked the box, and voila, suddenly I had no problems with seeing windows that should properly overlap mIRC.
so I'm trying to say, thanks for you advice, it gave me inspiration to work my problem out