First, if you're using DOS-type files, the lines are separated by "\r\n" instead of just "\n". You might have to tackle this as well. Of course, were you on one of those systems, your $/ would be set accordingly. Try this?

$lines =~ s#($/)+#$/#g;

The /m and /s flags seem to be a little extraneous given your specific circumstances. /m is used to modify the behaviour of ^ and $ within the regex, /s to modify how . is processed. See perlre for more details.

As a note, this is virtually identical to some of the replies you received for remove blank lines with regex, so why you posted again is unclear.