Good questions! I can say that I am using Roots Organic and have for a couple of grows. I grow all organic, so I haven't used their nutrient line so take my thoughts with a grain of salt...
If you're consistently having trouble when you switch to flower and the leaves are yellowing from the bottom up it sounds like you may have a nitrogen deficiency. I'm never a fan of jumping to the 'nutrient' issues because usually it's something environmental so as long as your temp/RH/lighting/ventilation/circulation/watering practices are all in check, then the next thing to check are nutrient issues. (Sidenote: the flowering stage is more difficult than the veg stage. Problems creep up more often so don't feel bad!)
I've noticed that when growing organic, I often need to give more nitrogen during the veg stage to prevent deficiencies during flower. Next time, you might consider doing that as a preventative measure. Of course, make sure that your watering regime is in check as well since watering needs change throughout the plant's life. Make sure your lights are at the correct setting in regards to height and intensity - when you switch to flower, you generally need to reduce the distance from your plants and/or increase the intensity.
I won't go into much more detail since I don't use synthetic or liquid nutrients and I don't use Roots for anything other than my soil. Feel free to hit me up if you'd like more info!