When applying a gift to a Recurring Gift, the prompt may not appear. This will occur if the Recurring Gift has a transaction pending in a batch. There will be an icon of a hand over a piece of paper in the lower right corner of the Recurring Gift which reads "Transaction Pending' when you hover over it.
A pending transaction will also prevent a Cash gift from being applied to the Recurring Gift. When clicking Apply To the Pledge or Recurring gift option is grayed out due to the Pending Transaction.
Commit or delete the batch to release the pending transactions.