Yes, since I have a lot of allergies, I use a LOT of custom foods and I found Fitday to be less user friendly for putting that stuff in, and their database just doesn't have the selection.
Don't join the site (yearly membership) buy the desktop software, it's a one time cost(they jacked their prices and a membership is virtually the same price as the software). The database isn't quite as comprehensive, but it can be updated from the site and you can still create custom foods.