I have the same issue. Per the regulations you quote, the person asking the question should not have any penalties associated with his SEP-IRA (made $240k, contributed $50k, which is less than the 25% threshold). But TurboTax seems to not differentiate between a SEP-IRA and a traditional IRA. How can we ensure the software identifies these contributions as a SEP-IRA and therefore not subject to contribution limit penalties?
