This is a User Groups issue.
User groups do not inherit permissions from each other. This only gives you access to the user group object, not the objects the user group has permissions to. For more information see Working with User Groups in the Application Manager documentation.
Code changes relating to User Groups (roles) have been made to make AM more secure. Therefore, if you have upgraded from an older version of Applications Manager and you experience this issue, you will want to ensure that you add a User Group to the user that has access to the Agent first.
When you "inactivate" an Agent, you have to Edit the Agent and uncheck the Active button, then click Apply/Ok.
In order to Edit any object within AM, you must have Edit access to ALL of the objects assigned to that object (including User Groups). To resolve this, you would add the "non-edit" user group to your "edit" user group. You do not have to assign the non-edit user group to your User itself.