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Well, some of the messages were pruned!
Anyway, I think I fixed the deleting messages problem.
Chaging viewpmsg.php line 45 to
$_POST['msg_id'] = unserialize($_REQUEST['msg_id']);
Some how it was not working with $_POST:
$_POST['msg_id'] = unserialize($_POST['msg_id']);
because arrays like
a:1:{i:0;i:2317179;}
after the post become
a1i0i2317179
and were breaking the unserialize function.
I think it is server related, maybe gzip or other kind of compression. Anyone knows why this happens?