since the next match blends into the first one

Actually it doesn't.

use strict;
use warnings;
use Test::More tests => 2;

my $pos = match_positions ('GCTTCTTGC', 'AGCTTCTTGCGCTTCTT');
is ($pos, '2 9 ', 'Matched'); # This fails because you have only one o
+ccurrence.
$pos = match_positions ('GCG', 'AGCGCGT');
is ($pos, '2 4 ', 'Matched');

sub match_positions {
    my ($regexp, $sequence) = @_;

    my @positions = ( );
    while ( $sequence =~ m/$regexp/ig ) {
            my $newpos = pos($sequence) - length($&) + 1;
            push @positions, $newpos;
            pos($sequence) = $newpos;
    }
    return "@positions ";
}
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Update: fixed the test count to include the second easier-to-follow example.