Debugging external CC1310 with SMARTRF06 and UART

I am attempting to use the SMARTRF06 board with the 10-pin ARM Cortex Debug connector to program an external custom board with a CC1310 on it.  On the custom board, there is a separate UART and JTAG header.  I am able to program the CC1310 over JTAG without any issues, but when I try and write UART commands through a host application, I am not receiving them on the CC1310.  This is only when actively debugging the CC1310 through CCS though.  If I unplug the JTAG header, or even simply uncheck the "Connect Target" button in CCS the UART starts working again, and will even process buffered messages that I had sent before.  Any ideas why the two aren't working together?