You're running this under mod_perl or fastcgi? Cos I can't reproduce your findings using straight perl.

#! perl -sw
use 5.010;
use strict;
use Time::HiRes qw[ time ];;

sub x{
    open my $fh, '<', shift or die $!;
    my @AoA;
    push @AoA, [ split ',' ] while <$fh>;
    close $fh;
    return scalar @AoA;;
}

for ( 1 .. 5 ) {
    my $start = time;
    printf "Records: %d in %.3f seconds\n",
        x( sprintf 'junk%d.dat', 1+ ($_ & 1) ),
        time() - $start;
}
__END__
c:\test>junk
Records: 400000 in 5.884 seconds
Records: 300000 in 4.752 seconds
Records: 400000 in 4.599 seconds
Records: 300000 in 3.473 seconds
Records: 400000 in 4.569 seconds

c:\test>junk
Records: 400000 in 4.826 seconds
Records: 300000 in 3.408 seconds
Records: 400000 in 4.613 seconds
Records: 300000 in 3.481 seconds
Records: 400000 in 4.557 seconds
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