Liam,
The difference in the VI is not an issue, as this is done for all IVI drivers.
Please describe more about your 3499 setup. What modules do you have installed? Different modules require different initialization, so it would be helpful in isolating what's happening.
Due to the re-configurable nature of the instrument, I suggest using InitializeWithOptions, as it will allow you to specify which exact modules are installed. This is important since some of them return ambiguous identification. For example, 44470A and 44470D both return '44470' as their identification, so the driver is unable to determine which one you have, unless you specify it. The control help in InitializeWithOptions explains the syntax needed.
Thanks,
Bankim Tejani
Sof
tware Engineer
National Instruments