I've been getting these for years from my wife's farm. It's an annoying practice, and as you know TurboTax won't allow this. If you try to override by entering both boxes on one form, it just won't file the return. Intuit should alter the code so it will. Obviously the IRS accepts them, or accountants wouldn't be doing this.
If you can determine which activity the boxes are related to, business income or rental income, then enter them in the appropriate K1. If you don't know, you could ask the accountant. If neither of those work for you, then my solution has just been to pick one form for all the boxes and leave them blank on the other.
