Before any new site would get +100 rep so I could use the core features.
Now I have to link them, then disassociate them and relink them to get the +100 rep
Is this intended site behavior?
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There was a regression earlier this week with regards to auto-association and the +100 rep bonus.
It has been fixed, and I've gone through and fixed the bonus on all the affected accounts I can find. There may still be some out there, but a simple clear/re-associate will grant the bonus as expected.