The proximity circle is calculated from GPS positional data which is known to be not completely accurate. This source of potential error has been well known for quite a while.
It was the topic of long discussions between Mal Wright, Tom Chalko, Manfred Fuchs, myself and others when we changed to using the Doppler speed data (2007?). Manfred suggested we use the Doppler derived heading data for the proximity circle as he reasoned it should be more accurate. We tried it in GPS-Results, but unfortunately we got too many erroneous results. These were the consequence of a small error in the heading, usually during the gybe (where it is unfortunately more likely). If the the heading plotted a course slightly straighter than the true course even for one point, the track contuned to reflect this error on all subsequent points. In other words, the error in heading was not corrected in any way and this could result in the course being well outside the proximity circle according to the Doppler derived heading, but inside the proximity circle when calculated using the positional data.
This is one of reasons why we have always said that the Apha is a result that can not be completely relied upon to be always accurate and why there are not WGPSSRC records for this category.
We rely on our observations that positional accuracy is usually reasonably reliable over short periods, such as the time it takes to do an Alpha 500 so the error in position is usually fairly small. Unfortunately, this is not 100% reliable as you have found in your GPS comparison.
With the current state of technology regarding positional accuracy for normal GPS's, there is not much the can be done about this. The greatest potential increase in positional accuracy seems to be the use of RTK technology, but this seems to be some way off general availabliliy or acceptance at the moment. In the meantime, I think we are just stuck with this issue. We need to realise that if the Alpha is within a meter or two of the circle limits, it is more likely to be less reliable. Not much help to those of us who actually aim to be 'just' inside the circle.

Another potential source of confidence it to use more than one GPS. That way if they are both saying it was inside the circle you may be just a little more confident.
By far the best is to use the GPS(s) on your head where it has been shown to produce less errors in both Doppler speed and Position, especially during Alpha gybes.

I must add that over the years we have had quite a few instances where different analysis software give different results with the same track. (where the position is extremely close to the circle). We have generally had the policy that if one software accepts the run, then we also accept it. (And no, there is not one particular software that is known to accept more close results than any other!

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