ok guys. I had same issue about one hour ago and I’ve made my own investigation. I’ve checked everything and became mad a bit, but I decide to use Occam’s razor. so, I saw that my VPS Apache vhost config didn’t overrode this:
<Directory /var/www/example.com/>
AllowOverride All
</Directory>
and so my .htacces just hadn’t worked. when I fixed it – all permalinks begin working nice.
you have to have good understanding for Apache config context (or any else web-server) if you administrate your server by your own.