I have a question here. I have a manager package and when I upload to some org my permission sets no longer have permissions for standard objects, does anyone have any idea why this is happening?
You can't package standard object permissions. Packaging semantics of Profiles and Permission Sets are documented in the ISVforce Guide:
Do they include standard object permissions?
No. Also, you can’t include object permissions for a custom object in a master-detail relationship where the master is a standard object.
Standard object permissions are silently ignored during the packaging process.