Same problem with my partnership return. Sold house that had apartment as rental unit. Cant enter it as single real estate transaction as it calculates the capital gain wrong and I cant correct it manually on form. When I try to do it as two separate transactions as a capital asset sale it just does not feel like an accurate representation of the sale. If I have to I will handle it this way and let the cards fall where they may, I'm still reporting the capital gain which all partners will be taxed on as reported on the K1 accurately so who knows. Agree this should not be an issue with the software as this is not a unique situation.
