Thank you!
Sorry if it looks like I am shouting this is the way I have always done my variables. At least for me they are easier to spot.
I was using code from a previous script and was not entirely sure what it was doing.

$FILE1PKG{$PACKAGE1[0]}{$PACKAGE1$FILE1PKG[1]} = $_;

Changed to
$FILE1PKG{$PACKAGE1[0]}=$PACKAGE1[1];


Also thank you for keeping it simple! I now have most things working and understand my errors much better!

As for the output being different I just used the first few lines of input and after posting realized I forgot to limit this for testing.

#!/usr/bin/perl
#
## Define variables
#

$EMPTY="";

#
## Open file 1 for input and place contents into hash table
#
$FILENAME1 = shift;
open(FILE1,"./$FILENAME1") || die "USEAGE ./checker file1 file2\n";
  while(<FILE1>){
    @PACKAGE1 = split(',',$_,2);
    #$FILE1PKG{$PACKAGE1[0]}{$PACKAGE1[1]} = $_;
    $FILE1PKG{$PACKAGE1[0]}=$PACKAGE1[1];
    }
close FILE1;


#
## Open file 2 and compare the two this will create several outputs
#

$FILENAME2 = shift;
open(FILE2,"./$FILENAME2") || die "USEAGE ./checker file1 file2\n";
  while(<FILE2>){
    @PACKAGE2 = split(',',$_,2);
    $FILE2PKG{$PACKAGE2[0]}=$PACKAGE2[1];
    }
close FILE2;


#
## Read in hash and do comparisons
#

for  $MASTERPKG ( keys %FILE1PKG ){
  print "FILE1 PACKAGE: $MASTERPKG     VERSION: ",$FILE1PKG{$MASTERPKG
+};
  print "FILE2 PACKAGE: $MASTERPKG     VERSION: ",$FILE2PKG{$MASTERPKG
+};
  $VERSION1 = $FILE1PKG{$MASTERPKG};
  $VERSION2 = $FILE2PKG{$MASTERPKG};
  #print "\nVERSION1: $VERSION1 VERSION2: $VERSION2\n";
if  ($VERSION1 eq $VERSION2) {print "SAME\n"};
if  ($VERSION2 eq $EMPTY) {print "MISSING PACKAGE\n"};
if  (($VERSION1 ne $VERSION2) && ($VERSION2 ne $EMPTY)) {print "DIFFER
+ENT\n"};

}
[download]

All seems to be working as expected!

I also use caps when testing again I find it makes the output I am looking for stand out more

All who have responded thank you for your time and efforts!
Duck