Please accept our sincerest apologies for the delay in replying. Unfortunately, I regret to inform you, but SyncMate is compatible only with native Mac OS applications: Address Book (Contacts), iCal (Calendar) and Mail. It does not support 3-rd party tools for private information management.
Most probably, your Fantastical keeps calendars in Mac iCal only virtually, similar to iCloud service, and they are not accessible for SyncMate. That is why you can see them in the list, but the actual synchronization does not transfer any data.