I doubt this was a database error.
You say they were newly ripped so they could not have been already imported. This may not be true. If you ripped the tracks to an auto-import directory, they would have been imported. And when you rip with MC, they are always imported. Since I don't know exactly what you did, I can't say what happened.
You also say you remove and added them several times. This is telling, as MC maintains a list of files that you've removed, so that a) MC doesn't try to re-auto-import them, and b) so that when you manually re-import them, MC doesn't have to read all the tags, but instead can just pull the entries from the Removed database. Auto-import won't re-import files, by default, that you've manually removed.
If you want to work manually the way you are, you're probably going to want to learn some things work, such as Auto-Import and how it differs from manual imports, what happens when you remove files, and how MC goes about updating its database of tags when tags externally are changed.
You might just consider ripping in MC, tagging in MC, and living in MC unless there is a very good reason otherwise (and you understand the interactions of your external processes and MC).