I have mIRC properly saving/loading my channels across multiple monitors just fine. My mIRC runs on my second monitor. I just tested this with desktop windows / compact mode, and everything works there too.

Are you by any chance running any scripts?

What does the following line give you if you run it in mIRC?

Code:
//echo -a $os $version $beta $md5($mircexe,2) $file($mircexe).sig $script(0) $dll(0) $com(0)