de0u Thanks. That turned out to save me the hassle of factory reseting the phone and starting over seting things up without seedvault.
I was thinking that somehow whatever seedvault did, it did not restore the sms and mms correctly. So I figured, if I could just wipe that data and start over with a different sms/mms backup app, then I wouldn't need to factory reset. It turns out SMS Import/Export has a very handy wipe messages function.
Strangely, after I wiped the messages (which was very slow) sms/mms were still trying to populate the messaging app. I realized that seedvault probably was trying to automatically restore data (I guess since I kept clearing the storage on the messaging app and reinstalling it to try to reset things). So I had to delete the seedvault backup data I had copied to the phone. Then when I cleared data on the messaging app and resintalled it (and after having done the wipe with SMS Import/Export), all the messed up restored messages were gone and I was able to start over.
I used SMS Import/Export to backup the messages on my old phone and restore them on the new phone. It worked fine, but was extremely slow (it took more than four hours to restore my sms/mms). I think SMS Backup & Restore probably would have worked, since it has worked fine for me in the past. And it's quite a bit faster.
But anyway, the wipe function on SMS Import/Export was super helpful, so thanks!