I don't think you should be calling the initiate function which tells the scope to acquire when the default setting happens. And the default setting for an acquisition is probably a trigger. Try to manually acquire a waveform and then just run the fetch.
NO, NO, NO. Why do you want to run the initialize function? That will reset the scope unless you disable that. The initialize function does not need to be called!
This is a little late to be mentioning this, but this topic would be best suited for the Instrument Control (GPIB, Serial, VISA, IVI) board, as the Agilent oscilloscope is not an NI HIgh-Speed Digitizer. You may want to post there and link to this thread to get some additional help.
I don't believe there's a way to change topics after the post began. You can always create a new post and put in a link back to this one, explaining that you're looking for help that pertains to instrument control/communication.
Unfortunately, I'm not as familiar with that Agilent scope, so I cannot advise so well on your questions.
I tried searching for your new post in the Instrument Control forum (https://forums.ni.com/t5/Instrument-Control-GPIB-Serial/bd-p/140) but it doesn't look like you've asked the question there. I'll be glad to help out but I'd prefer if we kept the thread going on our Instr Control forum for future customers who might have similar questions. Could you post a link on this forum to your new thread and the referse so people can get the background on the issue?
Be sure to post what specific model of the 5000 series you are using and a quick summary of what you've already tried. In the meantime, however, have you tried running the triggering example that ships with the driver called Agilent 6000 Series Edge Triggered Acquisition.vi? If you run this VI do you still have to trigger twice? Also are you still getting old data with this shipping example?
