Just an idea, to maybe come closer to the problem, try to 
use Data::Dumper;

[download]
somewhere early in your script and add some debugging aids into the problematic sub, like 
sub get_remote_file {
      print "Retrieving data file...";
      my @site_data;
print Dumper( $conx );
      chomp( @site_data = `$conx` );
print Dumper( @site_data );
      if ( $? >> 8 ) {
        print "Failed!\n";
      } else{
        print "Success!\n";
      }
      for $line( @site_data ) {
        ( $name, $filepath, $mod, $md5 ) = split( "\,", $line );
        $site_data{$name} = ["$filepath", "$mod", "$md5"];
      }
      @site_data = ();
    }

[download]
Maybe that reveals something that would explain the different behavior of the first run compared with the subsequent ones.

In reply to Re: Processing data from SSH stream by Krambambuli
in thread Processing data from SSH stream by Spasticus

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