Adrian-
To see the error - login to the context that isn't syncing and issue "show ft config-error"
Scripts and SSL keys/certs are not synced over, they will cause an FT sync error. If that was what happened, then upload the files to the context, then toggle "ft auto-sync running-config" on the active context and it will re-try the sync.
If the issue was not key/cert or script related, get a TAC case open, it is extremely likely there is a bug involved.
Regards,
Chris