Once I did that things imported cleanly
Yep, that indicates what I thought was the case.
MC has a database called "Removed" which keeps track of files that have been deleted from the Library, and includes the metadata the Library had at the time of the deletion. If you delete a file from the Library then re-import it, MC uses the metadata from the removed database for the imported file. The intent of that is if you have updated metadata in the Library, but not all metadata is saved to the media file itself as tags, when you re-import a deleted file you get back all your metadata that would otherwise have been lost.
So if you imported a file that didn't have all tags, deleted it, fixed the file, and then re-imported it, MC would show the old incorrect metadata, unless you run "Update Library (from tags)" for the files after the re-import process. At least it is my understanding the MC doesn't re-read the tags in the file when such a file is re-imported, or more correctly, it might read the file but will not overwrite the metadata it already has in the Removed Database. Anybody interested in knowing can test for themselves. Also, I don't think the "Update for external changes" setting in Auto Import will trigger tag updates in MC under this scenario, as there are no file events (which MC uses to identify when a file has changed) to trigger the update.
If you have deleted some files and want to do a clean import on them without using the Removed Database metadata, perhaps for just a few files, you can create a View limited to the Removed Database, then delete the records in there for the files in question, and MC will cleanly import the files next time you put them into a directory Auto Import monitors.
Of course it depends how you cleared the Library as well. If you just selected all files and deleted them, you haven't actually cleared the Library, and the Removed Database will now include all your files, with their old metadata. However if you used the "Clear Library" function under Playing Now, the Removed Database is also cleared, and you shouldn't have had a problem with the tags/metadata. You would then have gotten a "clean" re-import. I'm not sure if settings are cleared when using the "Clear Library" function though. If so, you would need to go through all settings again.
So, by deleting all MC Library files you deleted the Removed database, and then a new import process found the files and read the corrected tags, giving you a clean import.
Simple really, huh?