Hello,
Well, usually the ISR will detect what condition made it fire and then call something to take care of the interrupt. Most data transactions could be done by the ISR checking if it is in talk mode, listen mode, etc.
I would recommend adding some debug prints at the beginning and end of any routine that transmits data (including the SRQ). Perhaps the programmer has more than one place where data is transmitted. If you see any overlapping calls between a transmit routine and the SRQ, it will mean that there is an opportunity for the SRQ to mess up transmission.
I was not able to find any documentation about this chip on the Measurement Computing site. Have you contacted them for help? It may be possible that they have sample firmware or some other way to check the chip interface.
Steven T.