Try each of the following steps in order until the issue is resolved:
  1. Open the Recurring Gift whose transaction was not skipped to see if the Transaction Pending flag is present. If a transaction is pending in an uncommitted batch, the transaction cannot be skipped.
  2. Ensure the Next Transaction Due Date on the Transaction tab is a past date.  If the date the next transaction is after the one that should be skipped, then the skip will not process for this gift. 
  3. Change the Status to Active