Try using a port monitor program or split the serial cable to feed into an extra serial port to see if you can snoop on the communication between the PC and the device when you use their software. Maybe they are having those problems too and are supressing it. You would also be able to see if they are doing anything different in their communication commands and responses.
Your comment about the software provided by the vendor makes it sound as though the device stops communicating from time to time. If the device actually does that, then you need to monitor for the timeout error and retry after several seconds.
