Hello,
if you want to keep window position after restart mIRC: you must save position of the window (or all) on menu right-click -> position -> save (save all), on "window" button (treebar or switchbar or titlebar).
you can use a static position before join channel with:
//writeini $qt($mircini) windows #MyFavoriteChannel 100,800,800,400,0,0,0 | join #MyFavoriteChannel