The best suggestion I could give is to reach out to Product Support. They will be able to look at your situation more in-depth.
That said, you can also try to post this question in the Tableau Admin Community.
Hey Zottower. What's your architecture like? Are you running an HA environment, with Data Engine running on multiple hosts? Where are backgrounders running? How do CPU / network / disk utilization look like on your hosts? I ask because it seems possible that despite the extract refresh having completed, the actual .tde files haven't yet migrated to the Data Engine storage. This hasn't been a problem for us, but I can imagine it happening on a cluster with VMs that have had too much asked of them, for example.
Doing as Rody suggested and sending your issue to Support with logs and as many details as you can about when the data did / did not show up is probably your best bet--they can dive into what's happening behind the scenes.