Hi
Partially Granted means there are underlying security objects for this BI Report that are not granted to the permission set.
First look in the permission set detail window for this permission set and in the "Presentation Objects" tab , find the BI Report. (Use the search box on the page). Expand the BI Report presentation object and verify what objects that are not granted (checked), if any. This might give a hint. Compare with how the definition of the presentation object looks like in presentation object detail window.
Since the problem re-appears it is likely caused by a background process running nightly.
I'm not an expert on BI but there are cleanup jobs in the system that would revoke grants to objects that have been dropped / do not exist, even if temporary.
So one idea could be that the definition of the presentation object for the BI report refers to a non-existing / unknown object (perhaps some view)
Other idea is if the BI report meta data is automatically recreated and then access grants are lost in the process.
Since in test , are there any daily updates / imports of BI reports - might be good to verify as well.
If any of this does not help you to locate the problem I suggest to raise a ticket. Depending on version you are on there might be a resolution already for this.