I'm glad that you see your plugins now. I think a lot of users are getting confused about the difference between plugin layouts and the "All plugins" list as well as the functionality of Plugin manager vs the plugin browser. This seems to be leading to these sorts of problems.
For the record SONAR ships with a default layout selected that shows only the plugins that ship with SONAR in the box. If you want to see all your plugins (uncategorized) you must select the "Default - All plugins" choice. This item on that menu *dynamically* builds a layout from all the plugins on your system. When this is selected you will always see the latest scanned plugins.
Regarding plugin manager, it gives you a place to view all your plugins and to build *custom* layouts. You should only go there if you want to make a custom layout, hide/unhide plugins, or look at plugin properties etc. All normal operations, including selecting layouts should be done from the plugin browser itself. There is also no need to go there to scan, since SONAR does that automatically for you. Additionally, users should not turn on "rescan failed" and "rescan existing". Those choices defeat the whole purpose of fast scanning and are only provided for recovery and troubleshooting cases.