Thanks. I think I see what the problem is, but I need to reproduce it to be sure.
It doesn't happen for me when upgrading from 2.2.4 to 2.2.4, but when you upgrade from earlier versions, MODX actually performs all the intermediate upgrades one-by-one. One of the upgrades (I think 2.2.1) alters and saves the user object which fires OnUserBeforeSave, which triggers ActivationEmail at a point where the paths are not yet set properly.
At least that's my theory.
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