Hi,
You might try running your application on a Windows 2000/XP machine and enable DOS support. You can do this by going to MAX, and browse to >>Tools>>NI-488.2>>DOS Support... Now check the box to Enable DOS support for NI-488.2 applications. You should now be able to run your app from Windows 2000. Run NI-Spy before you run your application. NI-Spy should be able to capture all of the NI-488 calls that you are making.
If for some reason, you cannot run your app on Windows 2000, you could instead spy on the GPIB bus using a GPIB analyzer. This will allow you to capture all of the data that is being transferred over the GPIB. Hope that this helps.