I would use Iceberg to create your packages - it's free and much more reliable than Apple's PackageMaker:
http://s.sudre.free.fr/Software/Iceberg.html
It can also be scripted using the command line for automated package generation as part of continuous integration using Ant or similar.
Finally, if you don't need to install several things in different places (i.e. your application is a single bundle that just lives in the Applications folder or wherever the user wants to put it), consider not creating a PackageMaker installer at all - instead use a shrink-wrap disk image and allow the user to drag-install.