Make sure that you have entered the original Roth IRA contribution and then in the follow-up to that you have indicated that you switched from Roth to traditional. Entering it this way I don't see anything in either the online or the CD/download version that seems to imply a recharacterization from a traditional to Roth. Do not enter the contribution directly as a traditional IRA contribution.
Also note that the title of the next page, "Tell Us How Much You Transferred" is bogus. This page is actually asking how much was recharacterized from Roth to traditional, not how much was transferred.
