I own two Macs with an identical set of apps that both have the latest version of Mountain Lion (10.8.2). On one Mac, many of these apps register with Notification Center (NC). On the other, many do not. They just use Growl instead.
For example, Dropbox on Mac 1 is in NC. But on Mac 2, Dropbox is only in Growl. It will not show up in NC. Mac 1 also has Growl, but the apps "know" to register with NC as well.
I've tried reinstalling Dropbox after completely wiping its associated hidden files and it's still only registering with Growl and not NC. I'm also using the latest version of Growl.
Because Apple's NC implementation is a very closed system, I can't go in there and manually add Dropbox to the list or configure anything else. So I don't know what to do anymore...