OK, so just to clarify:
1. The dismiss button or "x" close button is not working. the notification is permanently stuck
Could you explain a bit more? Maybe list in order the steps you took to find the issue, like 1) I clicked on New Post 2) I clicked Add Media 3) etc.
2. also, my admin panels are showing the sub links when hovering...
Can you explain this more? The admin menus along the left side are supposed to hide their sublinks until you hover.
Also really helpful to know your browser version and OS version, and a link to your WP site if it's live.