There seems to be nothing in that piece of code that obviously relates to the problem you describe. Also you haven't told us the name of the variable you have a problem with, the name of the variable that works, and what values they're supposed to contain vs. what they actually contain. Could you post the code that shows how those variables are set and used?

Another thing that would help both us and you in debugging is if you can reduce the code with the problem down to a small, self-contained example that reproduces the problem.

More tips in How do I post a question effectively?

Sorry, as I said I am new to this. The variable I am having a problem with is $shipcountry, the variable $discnt works fine. I am trying to update $shipcountry via a form. It starts as "none" and I want it to change to whatever country is entered but what I end up with is, for example, "none, United States, Canada, United States" the number in the list depends on how many times you try and submit a change. I am not sure how I can make a self contained example but I will try.

Sorry, as I said I am new to this.

No problem, we're here to help. Pages such as "How do I post a question effectively?" are there to help people asking questions help the people answering them (despite their sometimes slightly patronizing titles).

I suspect the problem actually lies with the code that sets $shipcountry in your script. Are you using some kind of library to handle the input from the form? If so, I'd also look there for how it handles $shipcountry and why it might be appending the values.

A note on terminology for the future: A "list" in Perl is actually not what you've got with $shipcountry, that's a scalar (a single value) that contains a string (which happens to contain commas).

my(@LINES)=<REFFILE>; doesn't look right, you tried my @LINES = <REFFILE>; ?

Also, open (REFFILE,">$reffile") || print "Content-type: text/html\n\n Can't Open $reffile(r): $!\n"; appears to be wrong since, even if open() fails, the next line still tries to write to it - try open (REFFILE,">$reffile") || die "Content-type: text/html\n\n Can't Open $reffile(r): $!\n";

die goes to STDERR unless set up specially otherwise. So that ostensibly HTML error goes nowhere but server error logs, if even there; again by setup.

My point being, Your Mother, that the open failure could and indeed should, be better handled since if open() fails, the error log will get extended by the subsequent write failures.
A user level that continues to overstate my experience :-))

my(@LINES)=<REFFILE>; doesn't look right, you tried my @LINES = <REFFILE>; ?

In this case it's the same thing.

$ perl -MO=Deparse -e 'my @LINES=<REFFILE>; my(@LINES)=<REFFILE>;'
my(@LINES) = <REFFILE>;
my(@LINES) = <REFFILE>;
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The parens would make a difference if the thing on the left wasn't an array, and the thing on the right behaved differently in scalar and list context. In that case the parens would cause the thing on the right to be in list context. For example my $x = @foo; assigns the length of @foo to $x (scalar context), while my ($x) = @foo; assigns the first item of @foo to $x (list context). It's what makes sub { my ($arg0,$arg1,$arg2,@rest) = @_; ... } work.

original code:

open (REFFILE,"$reffile") || print "Content-type: text/html\n\n Can't 
+Open $reffile(r): $!\n";
my(@LINES)=<REFFILE>;
close(REFFILE);
$SIZE=@LINES;
open (REFFILE,">$reffile") || print "Content-type: text/html\n\n Can't
+ Open $reffile(r): $!\n";
print REFFILE "$date\| $ENV{'REMOTE_HOST'}\| $ENV{'HTTP_USER_AGENT'}\|
+$FORM{'discnt'}\|$FORM{'shipcountry'}\|\n";
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Step 1 - DO IT!

my $htmlheader = "Content-type: text/html\n\n";
open (REFFILE, '<', $reffile) || print "$htmlheader Can't Open $reffil
+e(r): $!\n";
[...]
open (REFFILE, '>', $reffile) || print "$htmlheader Can't Open $reffil
+e(r): $!\n";
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close(REFFILE)
  || print "$htmlheader Can't close filehandle for $reffile(r): $!\n";
[...]
print (REFFILE "$date\| $ENV{'REMOTE_HOST'}\| $ENV{'HTTP_USER_AGENT'}\
+|$FORM{'discnt'}\|$FORM{'shipcountry'}\|\n")
  || "$htmlheader Can't write to $reffile(r): $!\n";
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Step 2 - Recommended

my $htmlheader = "Content-type: text/html\n\n";
open REFFILE, '<', $reffile
  or print "$htmlheader Can't Open $reffile(r): $!\n";
my(@LINES)=<REFFILE>;
close REFFILE
  or print "$htmlheader Can't close filehandle for $reffile(r): $!\n";
$SIZE=@LINES;
open REFFILE, '>', $reffile
  or print "$htmlheader Can't Open $reffile(r): $!\n";
print REFFILE "$date\| $ENV{'REMOTE_HOST'}\| $ENV{'HTTP_USER_AGENT'}\|
+$FORM{'discnt'}\|$FORM{'shipcountry'}\|\n"
  or "$htmlheader Can't write to $reffile(r): $!\n";;
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Step 3 - Suggested

Additional suggestion: brace file handles '{fh}' when writing to them. It doesn't matter to perl, but it makes the difference between printing a variable and writing to a file handle more obvious.

my $htmlheader = "Content-type: text/html\n\n";
open my $fh_read, '<', $reffile
  or print "$htmlheader Can't Open $reffile(r): $!\n";
my(@LINES)=<$fh_read>;
close $fh_read
  or print "$htmlheader Can't close filehandle for $reffile(r): $!\n";
$SIZE=@LINES;
open $fh_write, '>', $reffile
  or print "$htmlheader Can't Open $reffile(r): $!\n";
print {$fh_write} "$date\| $ENV{'REMOTE_HOST'}\| $ENV{'HTTP_USER_AGENT
+'}\|$FORM{'discnt'}\|$FORM{'shipcountry'}\|\n"
  or "$htmlheader Can't write to $reffile(r): $!\n";
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more DO IT!

example scrubber for 'shipcountry'

my $shipcountry;
# shipcountry may contain letters, digits, underscores, spaces and das
+hes
# and nothing else
if ($FORM{'shipcountry'} =~ /^([\w -]+)$/) {
  $shipcountry = $1;
}
else {
  print "$htmlheader Invalid input for shipping country detected!\n";
}
print {$fh_write} "$date\| $ENV{'REMOTE_HOST'}\| $ENV{'HTTP_USER_AGENT
+'}\|$FORM{'discnt'}\|$shipcountry\|\n"
  or "$htmlheader Can't write to $reffile(r): $!\n";
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Another important change is to control flow logic and code organization

open ... or die Error(...);

open ... or return ErrorPage(...);

If you can't open the file, don't try to read from it or write to it, end the subroutine (the code should be in subroutines

Don't generate your pages by interleaving print statements, make subroutines, so your program is

Main( @ARGV );
exit( 0 );
sub Main {
    my $q = CGI->new;
    print SomeKindOfPages( $q );
}
sub SomeKindOfPages {
    my( $q ) = @_;
    ...
    my( $headers, $body ) = ShippingEstimator( $q , ... );
    return $headers, $body;
}
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