Hi,
It's my first post (in reality I just registered to write solution, and I probably won't visit this page again for some time...)
The problem for not working "add to cart" is really simple with mod_rewrite turned on, and it is "relative script paths" and solution for this is very simple too. To do this there is need to only add slash in JavaScript file in function which is called when form is submitted.
To be precise in line when is created Ajax object witch send query.
Some example

, this is no good line ( file theme.js in com_virtuemart theme dir):
new Ajax('index2.php?ajax_request=1', opt).request();
I have corrected this to (and other places where the shlash was missing):
new Ajax('/index2.php?ajax_request=1', opt).request();
And that solved problem not working Add to cart button.
Ofc I have corrected this in all js files I found in theme.
Ps. sorry for my English