As others have said, it looks like you're probably accessing two different sets of variables called @source and @destination. One is the lexical set that you are creating with the "my" call at the start of the loop and the other is the package variable set that you are setting in the "get_elements" call.

The two best pieces of advice that I can give you are:

1. Stop relying on side-effects to populate global variables
2. Turn on "use strict" and "use warnings" so you can see where you are unwittingly using package variables

Dave.

believe me: they get filled. the really get filled, because 99% of the time the scripts works perfectly.
--
to ask a question is a moment of shame
to remain ignorant is a lifelong shame

I assume you're saying that because you're accessing the data again in "scan_matrix". So here's what's really happening.

1. Each time round the loop new lexical variables are created by the "my" call.
2. You then call "get_elements" which puts data into the _package_ variables called @source and @destination, _not_ the lexical variables that you have created.
3. You then call "scan_matrix" which also accesses the _package_ variable versions.
4. You then use "undef" in your main loop which effects the _lexical_ versions of the variables.
5. The loop ends and your lexical variables go out of scope and are destroyed. The package variables, however, still exist and still contain the data that "get_elements" put in them.
6. The loop executes again and the process repeats.
--
<http://www.dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg

yeah, but like i said in a previous reply: i didnt and i explained why... bear with me these beginner mistakes, ok?
btw: strict will _show_ the problems i have, not solve :-p i will have to do the solving part, if i'm smart enough..

--
to ask a question is a moment of shame
to remain ignorant is a lifelong shame

How is get_elements filling @source and @destination if they're not being passed to it and they're lexical variables with visibility only in your loop?

It might help to see more of the code.

for my $mode (@probe_modes) {
   local (@source,@destination);
   create_map_file $mode;
   get_elements; # @source and @destination are filled here
   scan_matrix $mode;
   @source =();
   @destination =();
}

:-D you're about to be spanked! read previous replies above...
--
to ask a question is a moment of shame
to remain ignorant is a lifelong shame

Which is a quick hack the OP indeed had already found himself. Still it is nothing but byzantine logic to avoid what parameter passing is exactly for.

Ciao ciao!

#!/usr/bin/perl

use strict;

foreach my $item ('top', 'heavy', 'fool') {
    my (@array1, @array2);

    a_function($item);

    print "@array1\n";
    print "@array2\n";
}

sub a_function {
    my $item = shift;

    push @array1, 'crap';
    push @array2, 'dumb';
}
[download]

Global symbol "@array1" requires explicit package name at ./test_loop.
+pl line 18.
Global symbol "@array2" requires explicit package name at ./test_loop.
+pl line 19.
Execution of ./test_loop.pl aborted due to compilation errors.
[download]

...
my (@array1, @array2);

foreach my $item ('top', 'heavy', 'fool') {
...
[download]

ah thanks!
this was a really cool answer, learned much from it. like: test your code in smaller in pieces if you have a problem. i always seem to write too much at once, leaving these error hard to find. but like i really really realy learned today: _always_ use strict; and use warnings;.

again: many thanks to everybody who replied and devoted me. many new insights were given and i developed -i think- a new coding style. i can't say this enough: thanks!

--
to ask a question is a moment of shame
to remain ignorant is a lifelong shame

What if the subroutines had been exported from another package?

In this case your best bet would be to declare my (@array1, @array2) before the for loop if you want them to be available to your subroutines.

[SNIP]

This clearly tells me that the subroutine is looking for global variables. Declaring them as my inside a loop doesn't create global variables. So moving them to the top, like this, works fine:

OTOH this suggestion, in this form may contribute to suggest the OP to declare all of his own variables at the top of his scripts, which is indeed a bad habit many newbies have, and goes against proper scoping of variables.

I do use stuff like

{
    my $var;
    sub bus {
        $var++;
    }
}
[download]

myself, occasionally. But not as an alternative to parameter passing...