Script works fine for me but I don't have your text file. Im curious what's in it. If the text file is ok it's probably another script that is crashing your mIRC.

Try just running words from the text file through the scramble alias.

Run this to check scrambling every word in your text file.
Code:
alias test_s {
if (!$window(@test_s)) { window -e @test_s }
var %ty = $lines(wl.txt), %tn | while (%ty) {
%tn = $read(wl.txt,%ty)
echo @test_s %tn :-: $scramble(%tn)
dec %ty
}
}