The PacketShaper does support window scaling, so the shaping functionality will work fine.
The PCAP's window size data indicates too small of a value when you take the PCAP. There are two possibilities:
As an example, if the scale factor is 3, and the packet capture is showing a window size of 365, it means the window size is 365 * 2^3 = 365 * 8, or 2920 bytes.
For WireShark to show the real window size (window size * scaling factor), set Edit / Preference / Protocols / TCP / Relative sequence numbers and window scaling.