Are you using the same port for bar code scanner and the online monitoring via the PC? If so, then the command sent out by your PLC (meant for the bar code reader) interferes with the response the TRILOGI software expect.
The better method is to use COMM3 for online monitoring (using an Auto485 adapter ) while COMM1 is used for connection to the barcode. However, if you don't have an Auto485 adapter, then you have no choice but to use the same port to perform both online monitoring and connect to the barcode scanner (one at a time of course). But you have to use an input to selectively enable/disable the PLC from sending out data from its COMM1 port.
i.e. If the COMM1 is connected to the PC for online monitoring, then turn ON an input to disable the PLC from attemtpting to send out the data via COMM1. When the PLC is connected to the barcode scanner, then turn OFF that input so that the PLC is now allowed to send out data to the barcode scanner via COMM1.