Hi Jhon - Happy New Year!
As far as I'm aware, the high pitched sound has no other purpose other than to indicate that the chamber is flushing, hold in air. More important is that you can here the fan in the SRC whirring, indicating that it is working and indeed mixing the air inside the SRC.
Do you have access to another EGM and SRC unit? If so, it would be nice to take repeat measurements and check for agreement. If not, do you know when the EGM was last serviced/re-calibrated? Have you troubleshooted everything else (p73 of manual) such as checking if the soda lime needs replacing? It should be replaced if 2/3's of it in the tube is turning brown. It's hard to know if what you are seeing is the machine or indeed real measurements, but if you suspect it to be faulty, you can send it back to Oxford and we can get it fully serviced by PP Systems for you.
For the control experiment in order to calculate NV or pre-existing spatial variation, I don't think it matters too much that you are measuring this at a later date - we can assume that the spatial variation is the same now as it was then - perhaps just try to carry out the measurements in a similar time of year so that soil moisture levels are similar.
As for the analysis, I will try to find out where this is described in detail and get back to you.