This is what I've done so far, and everything I can think to test has seemed fine. It's a slight variation on what someone else posted in a different thread.
Backup your Addons folder
Install Ace updater (available at
http://www.wowace.com/wiki/WinAceUpdater)
Open up the Ace Updater and choose "Edit", "Mark Installed Addons"
Choose "File", "Install/Update marked addons with externals"
That has worked beautifully for me so far, including Mazzify's on new characters, as well as SCT, Autobar, Cartographer, and a few other "trouble" mods reported. The only hiccup I've had is an error generated when I convert to a raid, though it appears to have no impact on the frames or it's function. The error is below if anyone is interested:
1.0\MazzleUI_UnitFrames.lua:343: attempt to index field 'GroupFilter' (a nil value)
Also, this may only apply to a small fraction of you, but if you use the RC/beta releases of Atlas/Atlasloot, be sure to uncheck those mods in the AceUpdater before updating so you don't get reverted back to an older release version.