34980a scan rate

Hi,

I am trying to use 34980a Switch with 34922a mux modules to collect DC voltages. 

Here is how I am trying to achieve the intended data collection:

Step 1: Initialize the switch, reset it, configure it to measure DC Voltages and then configure scan with sweep count of 1.

Step 2: Inside the for loop, format the reading, initialize the scan, then fetch the readings. I loop 4 times, each time getting 480 DC voltages.

Issue: first loop the scan runs at a much slower rate. 480 readings take about 2 minutes. The 2nd, 3rd and 4th loop, the scan runs much faster. Less than 30 seconds per scan. 

Why do I have this scan rate issue? Eventually I need to collect close to 5K voltage readings so I cannot live with 2 mintues per 480 readings. 

If I skip step #1 VI (init/rst/config) and then run step 2 VI only, then all 4 scan loops run fast. I am quite confused.

Mahesh