Maybe you are overwriting $1, your loop seems strange to me

while (<ISH>){
my $a;
my $b = '#';
my $c;
my $x;
  if (m/DEV_STAGE\t(.*?)\n/g)        {$a= $1; print OUT "a is: ",$a}
  elsif (m/PREDICTED_GENE\t(.*?)\n/g){$b =$1; print OUT "b is: ",$b}
  elsif (m/\tSTAINED_REGION:\t(.*?)\tSTAINED_MOL:\t(.*?)\n/g) {
             $c = $1; print OUT "c is: ",$c;
             $x = $2; print OUT "x is: ",$x;
             }   
  else {}
}
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but your real problem is probably this:

You make a first pass to the loop and print to OUT

Then you examine the second line, make a second loop and OVERWRITE the output file with the actual values, $a is lost now

Then you make a third pass and OVERWRITE AGAIN, $b is lost... etc

Solution: use '>>' instead '>' and put each print inside its own if-elsif block

I started this before the other PMs gave an answer, so this is just another way to do it!

use strict;
use warnings;

my $ish = $ARGV[0];
if ( ! defined $ish ) { die "1: $!"; }     ## It helps to know which d
+ie?

open (ISH, "<", $ish) || die "2: $!";
open (OUT, ">", "out.txt") || die "3: $!";
open (my $LOG, ">", "log.txt") || die "4: $!";

#  $/ = "//";
   my $no = 0; our %hash = ();

while (<ISH>)
{  my $var = $_; $no++;
   print $LOG "$no\t$var";  ## This is to help know that you are readi
+ng and what it is
   chomp($var);
   if ( $var eq "//" )
   {  if ( %hash )
      {    my ( $a, $b, $c, $x ) = Process_Hash();
           ## You could do more work on %hash here or move the sub her
+e
           print OUT "$b\t$a\t$c\t$x\n";
      }
      %hash = ();     ## Clear %hash for next sequence
      next;
   }
   ## Note: If you data contains real tabs (0x09), then make the '\\' 
+a '\'
   my ( $key, $value ) = split(/\\t/,$var );
   #    print $LOG "\t$var => |$key|$value|\n";
   $hash{ $key } = $value;
}
if ( %hash )
      {    my ( $a, $b, $c, $x ) = Process_Hash();
           ## You could do more work on %hash here or move the sub her
+e
           print OUT "$b\t$a\t$c\t$x\n";
      }

exit;    # optional but I like to see it and be able to search on.


##     Process the element of %hash
sub Process_Hash
{  my ( $a, $b, $c, $x ) = ( "", "#", "for-you", "for-you" );
   if ( defined $hash{"DEV_STAGE"} )
        { $a = $hash{"DEV_STAGE"}; }

   if ( defined $hash{"PREDICTED_GENE"} )
    { $b = $hash{"PREDICTED_GENE"}; }

#    while (m/\tSTAINED_REGION:\\t(.*?)\tSTAINED_MOL:\t(.*?)\n/g)

    return( $a, $b, $c, $x );

}

1;
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If you start using hashes, you'll find that they save you a lot of code and help solve some very difficult problems. But there is no right or wrong, as long as it works correctly. Also, I left in the script the log that helped me figure what you were trying to do. Using a log will help you generate solid code. Delete or comment out when it's working the way you want. I usually declare a '$Debug' variable with a debug value. Once it works, I just declare

my $Debug = 0;     ## 0-Clean  1-light debugging  2- ...
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That way, if I working on or adding to the script, I can set $Debug to 4, and have a log of what's going on. (Note: This is my technique and not necessarily what others would do.)

Good Luck!