At times yes. I have noticed this error even when running the script on Vugen. But now i see this error on BPM too often.
To give you more insight into how this monitoring is set up. I have the thick client application installed on one of the point of presence machines and am running the script from another one (where BPM is installed).
For 2nd and 3rd, could you check whether there're long think time, or pacing betwteen iterations, and try to reduce the waiting time? If some operation need long time, you can increase the timeout value in the sync steps.