Hi maeco,
Could you tell me which versions of NI-DAQmx and NI-488.2 you have? Also, are you distributing an installer or an executable to the customer? Which version of LabVIEW was this developed on?
It's going to be really difficult to isolate what is causing the issue here. Will it be possible to try and eliminate either the USB-DAQ (CompactDAQ?) or USB-GPIB from the code to see if the behavior occurs?
Let us know, thanks!
Rasheel