i can confirm that the fix works on 3.0 but its on a 2g iphone. Havent tried the 3g yet.
There have been a few off topic questions regarding the popup when you are using something not designed for iPhone even if it is working. (some type of dock connector)
there is a new application called PopUp blocker that blocks all kinds of annoying apple popups.
go to cydia and add this repository
http://david.ashman.com/beta/
then look for the app PopUp blocker. Install that and then go to Settings and scroll down til you see the settings for it.
remember it is in Beta though but it is working well for me