Traffic appears to be flowing through PacketShaper, but the unit can't be accessed for management purposes.
PacketShaper cannot reply to 802.1q formatted packets. Therefore, when a unit is installed between two devices with 802.1q trunking enabled, PacketShaper cannot be managed from any client that resides within a VLAN, unless that VLAN is the"native" VLAN (no VLAN tag).
Since the switch/router does not put 802.1q tags on packets using the native VLAN, you will be able to communicate with a PacketShaper from another station on the native VLAN. You will also be able to communicate with the PS from stations on different VLANs as long as those hosts are routed through the router and PS is in Native VLAN. (The bottom line: when PS receives a VLAN tagged packet, it cannot respond with the necessary VLAN tags and the packet may not reach the end destination.)
If a PacketShaper is installed on an ISL trunk, you will not be able to communicate with PacketShaper in the trunk link. You need to install a LEM and access PacketShaper through the LEM (or use the built-in management port, availabe in certain models).