I think I finally have this resolved. I went through and uninstalled/installed a bunch of my extenstions. Took a while cause I have all of them.
I would like to make a suggestion for us users. It would be nice to have a column that tells what packaged extension an extension is part of. That way when I'm looking at my Downloads page and I see CSS Menu Writer, if I could see right there that the extension is in Design Extender then I know I need to uninstall CSS Menu Writer if I have Design Extender. Then I can reinstall or install Design Extender. That way I wouldn't have to go to other pages to see that, and sometimes its not easily identifiable. I think you should simplify it.
You could also show what version of the extension is in the packaged one. So maybe individually CSS Menu Writer is at version 2.0.6 but it may be version 2.0.10 in Design Extender. Then people know that in order to keep up they should purchase Design Extender.
The above is just an example. Hopefully it meakes sense.