A subset of transactions (typically those with gas usage in the millions) sometimes do not appear on Etherscan immediately. Although Etherscan takes time to reflect the transaction, the blockchain state (balances, storage in contracts, etc) gets updated as soon as the transaction is confirmed.
This discrepancy is due to the difficulty of tracing such huge transactions. The transaction is processed correctly, the state changes, but Etherscan takes time until the transaction is fully processed and visible.
We are actively working with the Etherscan team to improve the performance of tracing.