I didn't read the release notes a few updates ago, and I've been having the purple addons have been overwritten with an older version for several weeks. However, my roster was working just fine, so I ignored it.

This time, before the most recent patch, I decided to follow your instructions to uninstall all the bundled addons. Unfortunately, I didn't seem to have that option exactly so what I did was deactivate all the bundled add ons. That left me with a red square and a purple square in the manage addons page. It doesn't let me click on the purple square, and just gives me a notice to update to the most current version.

OK, so then I updated to the latest version of the beta via the zip file given to me by RosterDiag. (very nice function, btw) Now, when I surf to my members list page, I get "The addon [memberslist] has been disabled because it needs to be upgraded
Click to Upgrade 2.0.0.0 to 1.9.9.1479." How do I go about "upgrading" my addons?

nvm! I found it in the forums already. I had read the topic a while back but ignored it b/c everything was working. (lazy me)
http://www.wowroster.net/Forums/viewtopic/t=4611.html
The only thing I had to do differently was update the database entries to 1.9.9.1 b/c 1.9.9.14xx was registering as newer than 1.9.9.4