I am having the EXACT same issue. Prestashop 1.6.0.6
If you refresh in Firefox, you can see the correct product total flash for a quick second and then it goes back to $0.00. I know it is Javascript related but I cannot seem to pinpoint a fix just yet.
Again, this is only happening to products with combinations to them.
http://dev.gripnripracing.com/index.php?id_product=9&controller=product&id_lang=1#/select_mount-standard_1g_ft_w02