This looks like the metadata side of things has gone slightly awry as part of the latest release. I don't think the site guest user side of things is a factor, as that information is associated with the user record, not the permission set itself.
I have an old copy of a project in eclipse and the permission set files have the field accessibility for every field on every object (most are set to false, as I'm using it to provide access to a very small set of functionality). The files are huge and look very much like the profile files.
I've then refreshed this from the server and all of the field/object information has disappeared. This happens regardless of whether I tie the permission set to a specific license or make it organization-wide.
If I then deploy this permission set to my target org via eclipse, the object/field permissions disappear. However, if I use change sets it goes across fine. This is again regardless of whether I tie it to a particular license or not.
What is odd is that if I retrieve the permission set xml using the Force.com migration tool, all of the object and field information comes across. I originally suspected that the version number in package.xml was to blame, as eclipse will hit the endpoint supported by the plugin, but that's not the case as the version is 25.0 for both eclipse and the migration tool.