Oscilloscope .csv file output?

Im relatively new to this and am learning as i go. Dont have any background in electronic engineering.
Im using an Agilent Infiniium MSO8104A to record the voltage of the stepper motor control within a CNC milling machine and to record the movements of the x-axis and y-axis movements of the machine. I have circuits set up and probes attached. But i am also using a pre-amplifier circuit with a micro magnetic sensor to read the magnetic field of a PCB while the other axes are being read.
I am hoping to take an image of the PCB's magnetic field just for research purposes.
Problem:
I have everything set up and the Oscilloscope is reading everything accurately
Green = X-Axis
Purple = Y-Axis
Yellow = Magnetic field
http://i.imgur.com/8eYEecd.png
When i click File->Save->Waveform and save as a .CSV file then opening the file i expected to see 3 or 4 columns. 1 column representing the voltages being detected on each channel and a 4th column for Time. However when i opened it i only had 2 columns of voltage data. Even when i only have 1 channel active taking a reading and save it to the .CSV file it still has 2 columns of data in the fole.
I can tell by the slight voltage fluctuations in one of the columns that that must be the magnetic sensor readings as the sensor would not be as accurate as the probes.
I have spent the last week trying to figure out why only 2 columns of data (assuming they represent 2 channels) are being recorded and not all 3 channels at the same time. Can anyone lend some advice on what i am doing wrong, as i have played around with the Oscilloscope settings, read through most of the manual and i feel i am wasting far to much time on trying to figure this out. I have talked to a few people that are educated and qualified in electronic engineering and are more than familiar with the use of Oscilloscopes but have only been able to explain to them my issue. The lab i am working in is restricted so i can not bring one in to show them what i am doing and for them to walk me through fixing this issue. They have advised that it is really dependant on how you have your Oscilloscope set up and what it is i am trying to do. This Oscilloscope was set up for me prior to me commencing, so i have assumed it was set up for what i needed to be doing.
http://i.imgur.com/8eYEecd.png

I don't see anything in this about actually controlling the instrument.  You might have better luck going to an Agilent forum and/or Agilent Tech support since it is strictly with their scope and manually operating it.
There are only two ways to tell somebody thanks: Kudos and Marked Solutions

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    Thank you very much for your usual support.
    Fred

    Hi Nisar,
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    Thank you very much!
    Fred

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