Hello @Ben Wosjke ,
since the first version of ADConnect, all accounts with a not verified domain are synchronized and defined with the default .onMicrosoft.com.
I suppose that a specific rule was done to filter only accounts with the correct domain, or perhaps only Organizational units with accounts well formed were synchronized.
Probably one of these filters have been lost after an update or a reinstallation of ADConnect. Sample of filtering are indicated in this page.
In your case, you should use attribute filtering on " userPrincipalName" using the operator "ENDSWITH" with the value "@AD.COM".
Regards,