First step is to enable flags.enable_pop_prefix_broadcast as described in Unconnected PoPs. Otherwise second POP and the devices in its zones may not receive prefix allocation.
Additionally disable MultiPoP/Relay port as PoPs are not in same Layer 2 domain.
Before we get to possible issues, can you please tell me if you intend to enable Layer 2 in cnWave or use it in Layer 3 mode.