I think that the swatches are sorted by using the swatch name, if that is the case then the sorting will depend on how you have named each individual swatch.
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I encountered a simular problem, with my company swatches when i made them.
To fix it I had to asign color numbers to my swatches:
C12 daiquiri green
Maybe there is another way to establish a custom order, but I havn't been able to find it.
That's an interesting solution, thanks for the insight. Somehow my swatch reverted to the original order, though I have no idea what I did. I reloaded it a few times and was playing around with settings to no avail, but when I came back in the morning and opened AI it was back to the original.
If I can ever replicate it I will let you know, though I won't be hitting "sort by" anytime soon .
Thanks for your help.