Previously in Traveller it was only possible to have rule based fees apply to non-ITX tickets, since 6824 a new global option has been included to allow the consideration of fees on all ticket types.
To enable this option, select Options / Tools -> Global Options -> Costs and Fees, the option can be found near the bottom of the screen (Shown Below)
A tick in this box indicates that Traveller will consider rule fees on all tickets.