Isn't it easier to just switch over to $1 and $2 at this point? Your new substr workaround isn't very readable (to me anyway), so it appears that you've lost the one thing you were hoping to gain by using %+.

my $regexp = qr/(\d+)\s+(\d+)/;

while(<$fh>) {
    next unless /$regexp/;
    my $value1 = $1;
    my $value2 = $2;
    print "GOT $value1 $value2\n";
}
[download]