Really cannot tell the root cause without much more detail. However, these serial ports/devices *never* look for a certain "data pattern" and split it up based on that.
The application will do that. The data is simply returned as it is recieved from the PortServer.
My first guess would be flow control. Be sure flow control is implemented on the port and that it matches the attached device. Buffer overflow conditions can be monitored using DPA Remote or the "display port" command from the CLI.