Out of curiosity
@jmac75, was there a specific reason for using a normal Backup job instead of something like VeeamZIP over the list of machines? You can set a default retention there if you really want, encrypt, etc.
The GFS algorithms sort of are designed assuming that the job is gonna run, but it is a bit strange some didn't get flagged while others did. I half expect if you exclude the VMs that did get the GFS point temporarily and run an active full, likely the remaining backups will be flagged as GFS, but I'd rather recommend VeeamZIP if you're going this route since I think it's closer to what you're aiming for.
If you really need it to be GFS and it doesn't work with the above, open a support case and share logs from that job:
https://veeam.com/kb1832. Use the first radio option, select the job in question, and once the export completes, upload the logs to a case.