I don't know how this would affect the final product, but you're not sprouting them right. 12 hours is way too long for buckwheat. Check out the "Sprouting Instructions" here: http://sproutpeople.org/seeds/bwgroats.html
Hi - Well, for starters - you are not alone. Browse this forum or web enough and you'll find many stories similar to yours. The upset stomach is caused from a toxin which is produced when not properly sprouted. However, I've been doing this for 5 years, I know how to sprout the damn things, and still - every once in a while, I'll get a bad batch. To be honest, I stay away from them for that reason (drives me mad).
You'll know if they are bad, because they will usually taste a bit sour - dead giveaway.
For soaking, overnight is not a problem at all. If you're just trying to make buckwheat crunchies - You'll soak over night, rinse reaaaaallllly well, then spread on D sheet and let go until nice and crispy.
For sprouting, which I don't recommend. You'll treat just like any other seed you'd sprout - rinse 2-3 times a day, place in a ventilated container, colander, etc... But, like I said, Sprouted buckwheat is where you can get into trouble.
Furthermore, I know a lot of people who just have a hard time digesting buckwheat fresh or not. It doesn't matter if it's been masterfully soaked :) it will cause them horrific issues.
Any who, if you have any other questions, just shoot them my way!