We've just released VM extension version 2.0.40, which should correctly support manufacturers in categories and adding SKU to product page title.
Your problem with product flypage is most likely caused by wrong Itemid being stored with the URLs. You may use options in JoomSEF -> Manage Extensions -> VirtueMart -> Common tab to override VM Itemid with the preferred one (try using the ID of VM menu item, you can find it in Menu manager in Joomla). Make sure to delete already created SEF URLs in JoomSEF, so they can be recreated with new configuration.