if you want the window to appear after you've been nickalerted move "window -De @highlighter 0 0 450 160 arial 13" into the else statement
So
on *:text:*:#: { window -De @highlighter 0 0 450 160 arial 13
if ($me isin $1-) {
if ($chan == $active) { halt }
...
to
on *:text:*:#: {
if ($me isin $1-) {
if ($chan == $active) { halt }
else {
window -De @highlighter 0 0 450 160 arial 13
echo -t @highlighter 6* 13 $+ $nick 1called you at13 $time 1on channel13 $chan 1on the network13 $network 1and said6:13 $1-
....