One other major issue I've run into is getting projects to close when there is time on it from an inactive employee.  It will give you an error every time.  I found a work-around though.  If you temporarily reactivate your employee, and create a dummy paycheck for the employee for a couple hours of time, it will let you close the project and inactivate the customer.  Then delete the paycheck, and and inactivate your employee again.