With this scenario AJDT 2.0.0 works correctly. Newer versions work -almost- correctly too, but when package builder finishes the eclipse project keeps saying tha the project has errors (and it does not).
It's only when you refresh workspace state (F5) when errors dissapear. Even if you try to run the application in the emulator, aspects are working correctly and the 'X' marking errors in project icon dissapears. Maybe when you run/debug a project, workspace is syncronized with HDD.
I must say too that with AJDT 2.0.0 the 'x' marking error does not dissapear until the end of the building. It seems like it refreshes the view or runs builders two times. Dunno.