Allow me to jump into this conversation, rfish.
I'm here to provide more troubleshooting options to show all companies you've downloaded in QuickBooks Desktop.
Downloading your QuickBooks company files and setting the number of companies to 20 should show all of them. Since the problem persists, let's repair the software. Repairing replaces damaged installation files of the QuickBooks.
To repair, please follow these steps:
I also suggest saving all the downloaded company files to one folder you specified.
For further guidance, you can check out this article that will help: Fix QuickBooks Desktop (Windows).
From there, you shouldn't have any further issues. Please let me know how it goes by leaving a comment below. I'll be here to keep helping.