OK I know this is already solved but what is wrong with $.-- when you hit the !/^#/ and do the whole thing in one pass?

#!/usr/bin/perl

# comment
while(<>) {
if (/^#/) {
  print; $.--;
} else {
print "$.:$_";
 }
}
[download]

Run that on itself.

--
$you = new YOU;
honk() if $you->love(perl)