You have to quote the () in $skip, otherwise they're parsed as part of the regexp:

$file ="-(lala)-";
$skip ="-(lala)-";

print "$skip / $file\n";
if ($file =~ /\Q$skip\E/i) {     
print "matched!\n";
}
[download]

See quotemeta. You could also use \ if your pattern is static, just watch out for the double quotes eating it up:

$skip = "-\(lala\)-";  # $skip is now -(lala)-

compared with

$skip = '-\(lala\)-';  # $skip is now -\(lala\)-
[download]

-- Dan