Having lower number of holes is going to create a wider swing in high to low ratings but the overall average should be the same. In the U.S., the number of under-rated amateur players who are improving quickly can tend to depress ratings. If you are only seeing 1% difference, that alons might be enough to do it. The other thing you didn't mention is whether you disallow a player who shoots more than 60 points below their rating from being used as a propagator in the the SSA rating calculation? That will tend to boost ratings compared to not including them.
Rater of the tossed arc.