Question: Using a beaglebone black I seem to be having trouble getting the serial

Question: Using a beaglebone black I seem to be having trouble getting the serial pins to work. Using Adafruit_BBIO an dpython I can open the ports but writes do not show up. I have used an arduino to catch the data but nothing shows up. I can get data through ttyO0 but that ends up with activity during boot. I have even tried to enable the UARTs I need in the uEnv.txt but that still does not work. I am in as root so hardware permissions are not an issue. I have followed the Adafruit tutorials but still no results. Is the UARTs above ttyO0 on a different serial controller? I could have messed up my board experimenting. Any ideas? Thanks in advance.