This may occur once you've manually input and saved your keeper data, then re-synced your data with your league before the keepers were finalized (essentially overwriting your manual input).
This may also happen when syncing league data with a Yahoo! keeper league long before the draft because Yahoo doesn't send any keeper or draft order data until 30 minutes before the draft begins.
Therefore, syncing your league data with Yahoo! ahead of that 30 minute window will usually result in a loss of saved draft order and keeper data. However, league data will sync properly 30 minutes prior to the start of your draft.