Unfortunately, the QoS classifier of Zeroshell acts only in the FORWARD chain of the mangle table. The packets destined to the local processes of Zeroshell do not cross this chain and are automatically classified in the DEFAULT class.
To solve the problem you should remove the low bandwidth limit from the DEFAULT class and assign it to another class that you must create (for example with the name LIMITED). At this point, you just have to add a rule in the last position of the QoS classifier, without conditions and selecting the LIMITED class.
In this manner the traffic unclassified by specified rules is shaped by the LIMITED class.