The easy way out: Don't use PackageMaker. Create DMGs instead; your users will love you for it!
"Could not copy scripts" error
Remove all the script files from the package, and clear the script directory. Save your project and add everything again.
Absolute/relative paths option for scripts is disabled
Save your project first.
Cannot add custom files for interface because localizations is enabled
There's no way to disable localizations again; create your project again from scratch. Make sure not to switch to Raw Editing Mode unless you know how to use it.
Custom files in the interface stop working
I haven't figured out why this sometimes just gives up. Recreate your project and saving it should work.
Packages turn in to distributions
Packages can only have one choice; distributions must have at least two. Additionally, if you want to set up requirements or pre-/post-install actions, PackageMaker will create a distribution. If that's not what you want, write a script instead.
Installer doesn't change permissions
It's not a bug, it's just not clear that this is a feature. Select a package, then open the Package menu and take a look at Package options: "Overwrite package permissions"
Permissions are altered when building
I have no idea why it sometimes does this. I suggest you change the permissions of the package before you add it to PackageMaker to save you all the effort of changing it in there one file at a time (only to find out it changes it back when you build). Make sure to save before building.
The changed package contents aren't reflected in PackageMaker
Hopefully you can get away with PackageMaker not seeing the new contents; it will still copy the files from the source, you just can't see them in the Contents pane. If you need to change file permissions, you'll have to remove the package and painstakingly add it from the source again.