What could cause a VI to change its behaviour depending on if it was run in isolation or as a part of a larger program?

I have tried to collect a list of frequencies used from an Agilent 4294A impedance analyser. I have managed to collect the data but there are a number of additional null/zero values at the start of the list of frequencies. This only occurs if I use the VI within a program. If the VI is run in isolation it works perfectly. Does anyone have any ideas what could cause this behaviour?

Thanks in advance

Chris.