Hi,
The meta tags you set for articles are separate from meta tags you set in JoomSEF. If you set meta tags for new article, you don't see them in Manage Meta Tags in JoomSEF. Only if you let JoomSEF generate its own meta tags, or you set your custom meta tags in JoomSEF for SEF URL, then those are displayed in Manage Meta Tags.
The meta tags you set in JoomSEF overrides the meta tags you set for articles. So if you set your own meta tags directly for articles, they are correctly displayed on your website even when JoomSEF's meta tags are empty (Joomla handles this). But if you set your own meta tags (or let JoomSEF auto-generate some), those are then stored with SEF URLs and when you visit that URL, meta tags stored in JoomSEF overrides the ones coming from Joomla (from the article).