Summary: In Measurement Studio, NI488.2, a 40 second timeout works interactively, but transaction times out after only 10 seconds when running compiled program.
Detail: I'm zeroing and calibrating an Agilent RF Power Meter. When I run the Assistant in Measurement Studio, the 40 second timeout I programmed (40,000 msec.) works fine and the Query/Reply transactions with the RF Power Meter complete with good status returned. However, when the code is compiled with my program, the transaction times out after less than 10 seconds. The complete Microsoft Visual Studion C++ project is posted on my web site, complete with source code, NI's mxb files, and executable program.
See:
http://www.michaeltnelson.com/NI/Agilent_E4417A/