Hello wflynn,
Adding FileX to the threads tab automatically adds SDMMC block media driver and FileX Adaptation Framework, as well as relevant configuration. To use FileX on USB, you currently need to add it through the components tab (this should be improved in the future, once USBX Stacks are visible in the threads view).
As for the enumeration problem - I investigated this a little further to find that the valid FX_MEDIA instance is created, but it's not given media_id (hence it's not acknowledged as enabled by FileX API functions). This problem has been forwarded to the person responsible for integrating USB Mass Storage Host driver with Synergy.