If your contribution basis in your Roth IRA is more than $5,000, the distribution is not taxable or subject to penalty no matter what you did with the money and there is no need to claim the first-time homebuyer exception. You would only need to apply the first-time homebuyer exception to avoid any earnings distributed from being subject to an early-distribution penalty and possibly from income tax. Earnings are distributed only after all of your contributions have been distributed.
Make sure that you click the Continue button on the page that lists the Forms 1099-R that you have entered and answer all of the additional questions that follow, in particular the one that asks for your Roth IRA contribution basis.
