Good thought. Rather than using the debian packaged versions, I installed the following versions:

libnet-ssh2-perl               0.56-1
libssh2-1:amd64                1.5.0-2
libssh2-1-dev:amd64            1.5.0-2
[download]

libssh2 I pulled from debian unstable and did an SSB to jessie, libnet-ssh2-perl I pulled from CPAN and made a deb out of it. No change in the behavior.

I added the following code to play with the timeouts as VinsWorldcom suggested with no change in behavior:

 if ($model =~ /$nexus/) {
    my $output;
    $sok->timeout(10);
    @cmdoutput = $sok->cmd(
               String => "copy startup-config tftp://$tftp_server/$con
+figfile vrf $vrf\n\n\n",
               Errmode => "return",
              );
    print Dumper @cmdoutput;
    if ($sok->errmsg){
      ($error) = $sok->errmsg;
      print "Nexus IP: $host: Command failed reason: $error. Trying ag
+ain...\n" ;
      $sok->timeout(10);
      @cmdoutput = $sok->cmd(
                 String => "copy startup-config tftp://$tftp_server/$c
+onfigfile vrf management\n\n\n",
                 Errmode => "return",
                );
      $sok->waitfor (
             String => '#',
             Timeout => '5',
             Waitfor_clear => '1',
            );
      print Dumper @cmdoutput;
      print "Nexus IP: $host: Command failed reason: $error\n" ;
    }

  }
[download]