Your "port-channel" regexp sucked away matches for "interface port-channel", change the first regexp to "^port-channel" should resolve the regexp issue. Also why not use a more decent and easy to uderstand if-elsif structure.

use strict;
use warnings;

# $/="*\n"; 

my ($Rec,$pc_name);
my ($hash,$key);


while (<DATA>) 
{
    if (/^port-channel (\d+)$/) {
        $pc_name = $1;
    } elsif (m|(fc\d+/\d+)\s+\[(\w+)\]|) {
        $Rec->{$pc_name}->{$1} = $2;
    } elsif (/interface port-channel (\d+)/) {
        $key = $1;
    } elsif (/switchport description To (\w+) ([\d\.]+)/) {
        $hash->{$key}->{$1} = $2;
    }
}

for my $data (keys %{$Rec}) 
{
   print "\nPort-Channel $data : \n";
   for my $data2 (keys %{$Rec->{$data}})
   {
      print "\t$data2\n";
   }      
}

for my $data (keys %{$hash}) 
{
   print "\nInterface Port-Channel $data : \n";
   for my $data2 (keys %{$hash->{$data}})
   {
      print "\t$data2\n";
   }      
}
     

__DATA__
port-channel 1
    Administrative channel mode is on
    Operational channel mode is on
    Last membership update succeeded
    First operational port is fc1/5
    2 ports in total, 2 ports up
    Ports:   fc2/5    [up]  
             fc1/5    [up] *

port-channel 3
    Administrative channel mode is on
    Operational channel mode is on
    Last membership update succeeded
    First operational port is fc1/1
    1 port in total, 1 port up
    Ports:   fc1/1    [up] *

interface port-channel 1
  switchport trunk allowed vsan 1000
  switchport trunk allowed vsan add 1050
  switchport description To CCC219 10.33.81.56
  switchport mode E

interface port-channel 3
  switchport trunk allowed vsan 1000
  switchport trunk allowed vsan add 1010
  switchport trunk allowed vsan add 1050
  switchport trunk allowed vsan add 1900
  switchport description To CCC215 10.33.81.52
  switchport mode E
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