Since 1989, I have designed nutrition analysis software programs for several software companies. Unfortunately, the Windows and Palm OS products I designed are no longer available.
I would suggest you look for a nutrition analysis software program that has a dietitian works on development, closely scrutinizes the nutrient database, nutrients analyzed and features. Otherwise, you may be missing nutrient values or using inappropriate algorithms to calculate your nutrient analysis.
With my programmers, I developed My Food Record which has food analysis and 3 exercises tools with research-based algorithms along with updated food and exercise data. Other than that, there are nutrition professional software titles that run >$600 each that is used by dietitians such as Food Processor by ESHA Research.