Do you know the device identification for the on-board UART? What is it? Because I'm wondering if that is /dev/ttyUSB0 and your added USB serial is /dev/ttyUSB1.
A view of your system log from boot up and then insertion of your serial USB device would be helpful to see if you can post that.
You are correct that they should be 2 separate serial channels.
I don't see why uboot would have any relevance? You are running Linux at the time of these problems, correct?
Other things to check and report:
dmesg | grep tty >> tty.log
and then post that log; however the entire system log is likely more useful.