So update:
I removed everything again, Added everything back, not pulling info from anywhere. I selected "Add duplicates" and everything popped up fine, I went to through the process of correcting the tags to those on the launchbox database.
I closed Launchbox and when I opened it back up it's showing less titles now than before.
It's getting worse. Only the titles I didn't correct the tag to the launchbox database are showing up.