A collegue just emailed me furhter comments on this.
“Cosmic radiation has a diurnal cycle, but it isn’t completely in phase with sunlight. The magnetic field of the earth bends many of the rays (but not sunlight) so the daily peak is in the shifted. How much and in which direction depends on where you are in relation to the magnetic poles.
Then there is “space weather”. The flux of particles in earth’s vicinity is quite variable. See here: ( http://www.swpc.noaa.gov/today.html ) or here: ( http://spaceweather.com/ ) for recent levels and forecasts.
The usual procedure is to do calibration runs before and after the sample (or at the beginning and ending of the day for an eight-hour lab shift) and average the two for background subtraction from the test counts.”