Many-To-Many Report Issues

Can you confirm that as part of your relationship between Employees and Permissions that you have a 'Report Link' field enabled? In practice - you're report doesn't need any filters if you actually open it up in the Permissions table. So for example - lets say in the Permissions table you have a report called 'Embedded for Employees'. In practice - that report shouldn't be filtered on any one employee or any data except for things like maybe 'Active' or 'Valid' if you had some control fields. 

On your form then, and perhaps you already have it this way so if you do then maybe just confirm that your set up is like this -- when you display the report on the form you should be basing it on the report link field from your relationship. That then tells Quickbase to dynamically filter the records based on the Employee record you're viewing. You don't need to actually put any filters in the report itself, Quickbase does it temporarily for that view. The only filters that should appear on the report are those that apply globally for all employees - such as only showing 'valid' permissions as the example.

With that - one thing you want to make sure of though - is that if you open that report into a new window - you don't ever want to save that report as it is. Quickbase makes it a little too easy sometimes in the report page - that essentially you'd be overwriting it for the report as a whole which would create a filter issue with all other employees so you want to make sure you don't save the report with those filters in tact.