For anyone who may be interested, I could not figure out why it does not map atmel_rx_chars to an address in System.map. You can still set a breakpoint as normal in order to debug in this situation. I suppose it should have been more obvious when I was searching for answers. Anyway in the gdb command line type
b source_file.c:line#
so in this example, it would be
b atmel_serial.c:381
and it will break whenever you hit the "missing" routine. This is still an incomplete solution, though. Breaking into a specific line works but it doesn't leave the stack frame of the calling function (atmel_handle_receive), so locals of atmel_rx_chars are inaccessible to gdb. As always, any help or insight would be appreciated. Hope this serves as a good jumping off point if someone else ever runs into this problem or one like it.
Thank you,
Jayce