In a nutshell, if the fair market value of the like-kind property you received is less than the fair market value of the property you gave up, then the program will be looking for boot (property/cash/note/something-of-value you received to make up the difference).
If you do not enter the the "different" property as an equalizer, then the program will either through an error or not allow you to proceed. It would be helpful if you posted the figures for your exchange (even if they are hypothetical figures) here so we can determine if there is an input or software error.
If you need further assistance entering this transaction you should contact Support (link below) during regular business hours.
https://ttlc.intuit.com/community/using-turbotax/help/what-is-the-turbotax-phone-number/00/25632
