Are you drinking kefir made from REAL kefir grains or stuff from a box bought in a store? They are not the same, and only kefir made from grains has dozens of beneficial organisms with all of their beneits.
Benefical organisms need food, particularly fiber, to thrive. You have the right idea with FOS. But try oat and/or rice brain. Oat bran is cheap, delicious, and is full of fiber and other good things. Oat bran makes a wonderful warm porridge for breakfast.