That seems overly large for a logger... but I didn't go through it to try and see what all it did, so maybe not.
Anyhow, from the quick scan I did of it, all (or most) of the text being added to the window requires:
$mid($readini(mirc.ini,options,n4),$calc($pos($readini(mirc.ini,options,n4),$chr(44),12) - 1),1)
to equal "1".
So, I'd first check to see if it does... Type:
//echo -a $mid($readini(mirc.ini,options,n4),$calc($pos($readini(mirc.ini,options,n4),$chr(44),12) - 1),1)
See if it is 1. If not, that's your problem.