If I print "@$lines", I get this:

c1r1,c2r1,c3r1,c4r1,c5r1
c1r2,c2r2,c3r2,c4r2,c5r2
c1r3,c2r3,c3r3,c4r3,c5r3
[download]

but it only saves "c3r1" and comes out of the loop

This would happen if @$lines only has a single element, "c1r1,c2r1,c3r1,c4r1,c5r1\nc1r2,c2r2,c3r2,c4r2,c5r2\nc1r3,c2r3,c3r3,c4r3,c5r3". As I showed here, please use Data::Dumper to print out $lines, as in: "use Data::Dumper; $Data::Dumper::Useqq=1; print Dumper($lines);". If that shows a single string with \n's in it, then my assumption is correct. Instead of doing something like using split on that string, it's probably better if we took a look at where you're getting $lines from - please have a look at Short, Self-Contained, Correct Example, a SSCCE would be useful so we can run the code for ourselves and see exactly the issue you're having.

Here is SSCCE

#!/usr/bin/perl

use customlib;
my $file = 'cr.csv';


my $lines;

rdfile($file,\$lines);


# Remove comments and blank lines
@$lines = grep(!/^\s*#/,@$lines);
@$lines = grep(!/^\s*$/,@$lines);

@$lines = join "\n", @$lines;


my @store;
foreach my $line (@$lines) {
        my @val = split(/\,/,$line);
        push (@store,$val[2]);
}

#printf "@store\n";

use Data::Dumper;
$Data::Dumper::Useqq=1;
print Dumper($lines);
[download]

And you were right - @$lines with Data::Dumper printed the following output: $VAR1 = "c1r1,c2r1,c3r1,c4r1,c5r1\nc1r2,c2r2,c3r2,c4r2,c5r2\nc1r3,c2r3,c3r3,c4r3,c5r3" ;

Are you sure you showed us all the code?

Cheers Rolf
_{(addicted to the Perl Programming Language :)
Wikisyntax for the Monastery FootballPerl is like chess, only without the dice}