Below is the set of plots comparing measurements for the green and IR beat notes frequencies. The measurements were made on the spectrum analyzer at the same time. So I have not taken measurement error into account. 
From the plots, the discrepancy is not very large.

Attachment 1:
Shows the two sets of measurements scaterred along y=x.

Attachment 2:
Since plot 1 shows the points tightly scattered to y=x, I plotted the difference between the two measurements against their mean to blow out the deviations.

I will do the same comparison using the frequency counter readout once we have RF amplifiers installed.