Home Page "Add to Cart" & Quantitiy Buttons issues

Has anyone else been having this issue at all:
The "Add to cart" and "Quantity" buttons for products on home page dont work, in a way that quantitiy buttons dont work at all and "Add to Cart"buttons re-direct to www.mydomain.com/index.php and the cart still empty.
Now I have renamed the htaccess.txt to .htaccess and change the Apache rewrite and SEf to yes on the global congif and reverting those back did not change anything at all except that still the logo link is www.mydomain.com/index.php but all the other pages are without the index.php.
Also when I upgraded the VM to 2.6 version now the save cancel buttons on VM registration page are gone and the checkout page is a mess.....
Any idea what been happening her??

Last updates vm published with vm2 were very messy.
You can send us link so we have an look