Why are tabs I've pinned as apps still opening in regular tabs as well?

Tabs I've pinned as apps continue to open as regular tabs even though I closed them and reset my options in startup that when Firefox opens use current pages. This completely wastes the spacesaving benefit of this feature. Also, with the new version, I have lost the ability to drag URLs into my folders.

You would certainly get a duplicate if you have your home page as an app-tap and with When Firefox starts: Show my home page.
Any other problems might have to do with "Tab Mix Plus" or "NoScript" extensions.
I can drag tabs to folder in Firefox 5, so that problem must be an extension.
You can test quickly one shot without extension, using
* "Alt+H" (Help) > Restart with Add-ons Disabled...
When your problem is solved, you might find value in these two extensions for tabs.
* Add Bookmark Here ² :: Add-ons for Firefox<br>https://addons.mozilla.org/en-US/firefox/addon/add-bookmark-here-2/
* Multiple Tab Handler :: Add-ons for Firefox<br>https://addons.mozilla.org/en-US/firefox/addon/multiple-tab-handler/ <br>http://dmcritchie.mvps.org/firefox/multiple_tab_handler.txt

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