When a HDL package file is added to the project, the sources window for the project does not show the package file. The file is added to the synthesis ".prj" file so that the project works correctly, and the package file is included in the project, but the GUI does not show the added file.
After being added, the package is displayed in the Libraries view, but is not displayed in any of the synthesis or simulation views in the Sources window. The Association property on the file (in the Libraries tab) should be correctly set to "Synthesis/Imp + Simulation." As stated in the problem description, this is a visual problem only because the package does get properly processed when the design is synthesized or simulated.