I have a somewhat similar question. I took advantage of the option to roll pre-tax contributions that were made to a traditional IRA into my employers 401k (they allow it). I did this specifically so I could isolate and then roll out my after-tax contributions (from the same IRA ...yes, we had co-mingled pre and after tax contributions over the years) into my Roth IRA. I received two 1099-R's from Vanguard, one which shows the the pretax rollout to the 401K as not taxable (correct), but the second 1099-R shows the rollout to the Roth as taxable (not correct). Vanguard says they consider any rollouts from an IRA as taxable and have no way of knowing or differentiating pre from post tax contributions. I do recall when I processed the rollout to my Roth there were all sorts of messages asking me to swear this was after-tax money, so not sure why the 1099-R says the entire amount is taxable.
That said, how do I address this when I do my taxes, because that 1099-R will be incorrect.
