Part of it is probably related to your "payoff" amount. You can request this amount from your current lender. You tell them a future date that you will pay the mortgage off (either through a lump sum payment or a refinance), and they'll tell you what the payoff amount is. The amount is going to be higher than the current balance because interest is accruing every day. Depending on the number of days and the balance, this can add hundreds if not thousands of dollars more.
They probably also are requesting extra money to establish a new escrow account.
None of this has anything to do with it being a VA loan. This would happen with any refinance.