The situation which you have observed can be explained by the fact that serial ports are streaming devices and we cannot predict when the block of data being received will end. So, if the both applications (ports) are writing to the same COM port, the data from the two might get merged and the receiving party will be unable to correctly process them.
If you are able to modify your applications, we can recommend you to use a named mutex or other methods for synchronizing the serial communication.
As far as I know our technical support specialist Victoria is communicating with your on your further questions via email. Thanks for your attention to our products.