Hey gsflat,
It sounds like your application is having time problems, because SPY typically makes programs run slower. Depending on what language you are using you can try adding some additional wait to your application. If you are running a multiple thread application or LabVIEW code in parallel it is possible your code is getting into a race condition and SPY just happens to change the timing of the application execution.
I would try to reduce the application to see what specific addition to the code cause the problem and then try to find a way to work around it. Normally you can start with some shipping examples to verify that the devices are communicating without any problems or you can just start simplifying your application.
In some instances I hav
e seen computers that just ran too fast for the GPIB instruments to keep up and the same program would have errors when ran on a fast machine versus when it was ran on a slower machine. In these instances adding a little wait into the application fixed the problem.
I hope this helps out.
JoshuaP
National Instruments