If you use clear the position and do not save it at all, and then move/size the main mIRC window to where you want it, exit, and re-run mIRC, does it open up in the same place?

When a specific position is not saved, mIRC will always open up where it was last located when it exited.

If this does not work: if you move mIRC to the main display and try to save the position, does that work?