You mentioned that The file has links to other files in the package. How did those links get there? Were those links originally between PDF files in a relative folder structure? Then you put those PDF files into the PDF package?
Unfortunately, Acrobat 9 does not support hypertext linking between files in a PDF package.
You mentioned your lack of success getting the links from the second file in the PDF package. In your PackageFiles result element, you can specify the name of the file you want, but you cannot specify the ordinal number of the file. Here is a DDX that extracts a file from a package. The <NoPackage> changes the result from a PDF package to a single PDF.
The links are created using Acrobat 8 or 9 using a package. I go to one of the file, highlight some text and create link. When setting the link, I open another document in the package or portfolio and hit the SET LINK bottom. When I click on the link it works just fine in both 8 or 9. If I use PDF Can Opener or PDF Optimizer (Browse PDF structure), I can see the link with a GOTOE action for an Attached file. It works great - so I assume that is supported?
I tried extracting the file as you suggested, but when I do that, the GOTOE actions are gone - links point to Page 0. I assume it's because it is no longer in a package.
You're right; Acrobat can create links between docs in a package. I learned something from you.
I don't know why the GOTOE actions would be missing.