WinpkFilter driver works between TCP/IP stack and it’s bound adapters, it does not filter non TCP/IP interfaces. As I understand you miss packets which are routed by network bridge and never reach TCP/IP stack. This is just how it should work.
However, driver can be modified to additionally support filtering between the bridge and real network interfaces below the bridge, it just requires some modifications in driver itself. If you own Source Code license you can easily do required modifications yourself, I think it should be enough to add network bridge protocol name to the list of filtered protocols.