My Java application has a launcher which is a .app and a helper app which is bundled with it.
I am trying to make .pkg installer with a background image using the fo
I have had roughly the same problem. It appears that the OS X installer uses information about already installed packages and application bundles in order to decide where and if to install new packages. As a result, sometimes my installer did not install any files whatsoever, and sometimes it just overwrote the .app bundle in my build tree. Not necessarily the one used to build the installer, but any .app bundle that OS X had found. In order to get the installer to install the files properly I had to do two things:
Tell OS X to forget about the installed package
sudo pkgutil --forget
Not sure if this is needed for you nor in my case, but it is probably a good idea anyway.
Delete all existing .app bundles for the app. If I didn't do this, the existing app bundle was overwritten on install instead of the app being placed in /Applications. Maybe there is a way to prevent this while building the installer package, but I haven't found it.
If you can you should probably try to make your application self contained so that users can install it by just drag and dropping it into /Applications. Of course, this only works if you don't need to install anything outside of your .app bundle.