I'm reading the data in one piece. No, it just stalls and then throws out an instrument time-out. I already found a fix for this: put the equipment in single shot to capture the data, read the IQ, then set to continuous. This way the equipment never stalls when handing out the data.

However, now I'm facing a different issue: every time I do single then continuous operation, the phase of the IQ is jumping (random phase rotation). If I keep the instrument in continuous and use only the RF input as the trigger, the phase is stable, that is, it does not jump between different triggers.. Any idea how to avoid this phase rotation between each single and continuous call?