Hi there,
For those unknown… " BACnet stands for Building Automation and Control Networks. It is a communication protocol standard designed specifically to provide a way to integrate building control products made by different manufacturers ."
a close analogy is MQTT and often they compete, with MQTT security out performing in HUGE deployments. (cloud based).
Can you do a "LOOPBACK on the port? Is it a 4 wire RS-485 ?
Does the port use Hardware flow control ? Sounds like a driver issue in the stack or the baud rate clock on the internal port is drifting (garbage)
The dongle is using the USB, is probably why it works. Give a good visual inspection something may be loose in there…for such performance.
HTH
GL 
PJ 