Hi,
I am the OP. I had intended to reply to this some time ago, but got busy and then forgot

But I remembered now!
I believe the issue that we were having is that we were installing MODx on a new server, and then trying to point the new installation to the existing database. When this was done, usually the new install was a newer version than the original site we were moving. I guess we were getting ahead of ourselves with theories about how to make life easier. Basically what we found is that if upgrading and moving MODx sites, it’s best to move it AND THEN upgrade, OR, upgrade it AND THEN move it to the new server.
I’m dealing with a site now that has been hacked, and because of that we are moving it to a new server. The only thing I’m worried about is, whether I upgrade or move it first, I might be dragging some infected or non-stock files over with me to the new server. Any way to make sure the site is clean on a server move or upgrade? Does the upgrade over-write potentially "dirty" files?
Thanks for the help!