ubetido:

Nutritionally, they appear very similar to flaxseed.  And though they're trumpeted as being rich in minerals, they have a very high phytate content (like most seeds), so most of those minerals are not very bioavailable.  Add to that all the usual antinutrients in seeds and the fact that ALA is not easily converted to the long-chain n-3s that our body requires (particularly DHA), and I see no reason to consume them unless you're so poor that you can't afford meat and eggs.

Think of it this way.  What's likely to be more like a human, and provide more of a human's nutritional needs: a baby chicken (an egg), or a baby chia plant (a chia seed)?

JS

Not to my knowledge: phytate binds minerals, but it doesn't cause stomach upset AFAIK. 

My guess is that you're experiencing side effects from the trypsin inhibitors (or other protease inhibitors) in the raw seeds.  Seeds don't "want" to be eaten, and if eaten, they don't "want" to be digested: they generally contain chemicals that inhibit the digestive enzymes of animals, in hopes that they'll be pooped out while still able to germinate.  It's the same problem you'll get eating undercooked beans (don't do this...6-8 raw red beans will put you in the hospital).

JS

Heat often decreases the activity of protease inhibitors in seeds.  That's why raw beans are often poisonous or indigestible, whereas cooked beans can be eaten.  Roasted nuts are usually better than raw nuts, for the same reason.

Unfortunately, flax and chia seeds are generally consumed raw, because the ALA in them is very unstable under heat.  (This is why flaxseed oil goes rancid if you don't keep it cool and in the dark.)  Result: lots of antinutrients.

May I ask why you're eating chia seeds?  Our bodies don't need ALA: we use the longer-chain n-3s like EPA and DHA, and our bodies are very inefficient at upconverting ALA to DHA (less than 1%).

JS