I've confirmed that the CD/download version of TurboTax has the same bug, but with the CD/download version it's possible to get the correct taxable result with the single Form 1099-R by making entries in forms mode. To do so, it's necessary to mark the second box in the Inherited IRA section, "Recipient, but was originally inherited from a spouse (treated as recipient's IRA)," entering $4,000 as RMD, then entering $6,000 on line B2 in the Rollovers section. This combination of entries is not possible using step-by-step mode and if you edit the form in step-by-step mode after making the forms-mode entries, step-by-step mode will corrupt your forms-mode entries.
