Dear Conrado,
I have not tweaked the rr.conf file myself but my guess is that the UHD driver still points toward the same USRP, which is used with two transceivers. Looking at the enb.conf file used by Charm I notice this line which I have not noticed in regular configurations:
| device_args =
fail_on_disconnect=true,id=enb,tx_port0=tcp://*:2101,tx_port1=tcp://*:2201,rx_port0=tcp://localhost:2100,rx_port1=tcp://localhost:2200,id=enb
Have you tried to use the Charm configuration and software as is, instead of only importing selected files (maybe also with a different scenario)? For concerns specific to Charm the best way would be to contact the authors of the paper directly.
Regards,
Leonardo