The extras that I'm aware of use createObjectContainer(), which would use either the MODX charset or the DB charset -- not sure which.
What happened in my case was that the DB charset was somehow changed back to Latin1 a while back. I suspect that it happened in a server upgrade at the host.
Ironically, this thread prompted me to run SiteCheck again at Bob's Guides. The Quip, Dashboard, and Media Source tables were in Latin1. I just had to run my own database charset converter again on my own site.
It's worth having SiteCheck around just to check this periodically. It would be really easy to fix if you caught it before any new tables were created.