For a software vendor to make you take the actions you describe to trick buggy software so that you can use it is unprofessional and irresponsible on the part of Intuit. Given the aging US population, to not be able to differentiate between different 1099-r situations in tax software is unbelievable.
Sounds like you edited the worksheets to meet your needs. Did the calculations happen after you edited the worksheet to remove the error?
