If you look up crypt in perlfunc, you'll see this:

  When verifying an existing encrypted string you
  should use the encrypted text as the salt (like
  `crypt($plain, $crypted) eq $crypted').  This allows
  your code to work with the standard `crypt' and with
  more exotic implementations.
[download]

You have have used substr in your code to cut off just the salt. I don't have access to any FreeBSD box, so I can't test if this is really the problem, but I figured I should throw this in anyway just in case.