Difference between POA reported and weather file data

I am using SAM 2020.11.29 and the detailed PV calculation with default settings except for tilt angle set to zero and changing the weather data. 

The "Irradiance GHI from weather file" is different to the "POA front-side irradiance total nominal (kWh/yr)" divided by the total module area as shown below. 

Single values     Phoenix Des Moines Fargo Blythe
Annual Energy AC (year 1)   7679.08 5572.47 5430.7 7747.59
POA front-side irradiance total nominal 48292.1 34017.8 32012.9 49319.7
POA /m2      2114.923 1489.789 1401.986 2159.926
Irradiance GHI from weather file  2115.088 1498.681 1403.705 2175.18

These values should be the same? And any difference is either down to rounding or parsing of the weather file? I note that the largest difference here is for Blythe which also had the following log notes when running:
"Calculated negative global horizontal irradiance of -3.07184 W/m2 at time [y:2009 m:2 d:1 h:17 minute:30], set to zero.
Calculated negative global horizontal irradiance of -2.94782 W/m2 at time [y:2009 m:2 d:2 h:17 minute:30], set to zero.
Calculated negative global horizontal irradiance of -2.30415 W/m2 at time [y:2009 m:2 d:4 h:17 minute:30], set to zero.
Calculated negative global horizontal irradiance of -1.02942 W/m2 at time [y:2009 m:2 d:5 h:17 minute:30], set to zero."

I am also seeing larger differences between the reported POA/m2 and the weather file data when using custom files. These also had similar log notes to the above for Blythe.