hmmm... it seems to work just fine for me... Does this self contained script exhibit the errors when run in your environment?

#!/usr/bin/perl -wT
use strict;

while(<DATA>) {
  tr/\\\@/@/d;
  print if /USE/.../USE/ and !/USE/;
}

__DATA__
I like jellybeans
me too
begin USE information
options   [ --upload | --download | --commit ]
          [ --filename <filename> ]
          [ --list <list> ]
          [ --host <hostname> ]
          [ --server <ip/fqdn/hostname> ]
          [ --string <snmp community> ]
          [ --path <path within tftproot> ]
          [ --regex <regular expression> ]
          [ --version ]
          [ --verbose-help ]
          [ --help ]
end USE information
Still like jellybeans
me too

=output
options   [ --upload | --download | --commit ]
          [ --filename <filename> ]
          [ --list <list> ]
          [ --host <hostname> ]
          [ --server <ip/fqdn/hostname> ]
          [ --string <snmp community> ]
          [ --path <path within tftproot> ]
          [ --regex <regular expression> ]
          [ --version ]
          [ --verbose-help ]
          [ --help ]
[download]

-Blake