In the setup with 2 WR PTP Cores (v4.0) connected to the WR Switch v5.0, both nodes are synchronized. I restarted the switch (by executing reboot in the linux shell) and after booting up again, only one WRPC was synchronized, the other was stuck in listening not receiving any traffic.
Having a quick look in the WRS it looks that despite the link being up, no frames are sent on one of the ports. In SNMP, PTP Tx frames counter increments on that port, and also in Pstats NIC_Tx counter increments. However Tx frames counter in the Endpoint remains 0.
ifconfig wriX down; ifconfig wriX up fixes the problem.