Thanks for everyone's help here.  I have done some further sleuthing.

I have a second 53132A which has a 3.0GHz Channel 3.  So, I switched the new 
channel 3 board into the old 53132A and it reads properly.  Then, I switched 
the old 3.0GHz Channel 3 board into the new 53132A and it also read four times 
(4x) the input frequency.  From this I conclude that the issue is with the new 
53132A counter box and not the channel 3 board.

Then I powered up each counter and measured at the pins on the ribbon cable 
connector at the Channel 3 board to the main board on both the new and old 
counters (channel 3 boards plugged in and powered).  They each read the same 
voltages and/or grounds (pin1 = 2v; 2,5,7,9,10 = ground; 3,8 = +12v; 4 = -12v 
with numbering based on "1" shown on channel board).

Someone suggested that maybe the new main board had been set up for the 12.5 or 
6GHz channel 3 but was sold without that channel.  The idea was that such a 
main board would cause a 4x reading.  To my mind this is opposite to what I 
would think in that the division ratio for 12.5 or 6GHz would be higher than 
the ratio for the 3.0GHz board and would result in a fraction of the frequency 
rather than 4x frequency.  

Of course, it could be a FW mod (rather than a HW mod) which has been applied 
also.

Any other thoughts are much appreciated.

73,
Jim Robbins 
N1JR
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