I've developed a Pi-based internet gateway, which uses an XBee S2C coordinator in API mode to receive regular readings from a number of sensors in router API mode. The Xbee is wired directly to the Pi's UART ports, and takes a 3.3V supply from the Pi - so simple wiring.
I have this working on a number of identical gateway devices using S2 Xbees (with the small aerial) with no problems and exactly the same hardware and software setup.
The problem I have is that I have tried to switch to S2C modules, and on hardware shutdown and reboot, the coordinator attached to the Pi stops responding. It still appears as part of the network (using XCTU and another XBeee router with the same PAN ID), but when settings are queried wirelessly it is slow to respond before eventually timing out. The coordinator also fails to respond to any data being sent to it.
To make the coordinator function again I need to physically unplug it from the pi, plug it back in, and its fine again.
All modules are running the latest firmware.