Using mmap() just to get an aligned buffer seems like a bit of a sledgehammer and might be causing problems (though I don't have swapped in the implications of that particular use of mmap). You could try a different approach:
my $bufsize= 4096;
my $align= 512;
my $buf= 'x' x ($align+$bufsize);
my $off= unpack( "J", pack "p", $buf ) % $align;
$off= $align - $off
if $off;
sysread( $FH, $buf, $bufsize, $off )
or ...;
my $data= substr( $buf, $off, $bufsize );
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