I am guessing that you live in a climate that has multiple freeze/thaw cycles. everything moves with the weather conditions - expanding and contracting. additionally, if water somehow finds its way into the mortar or stone, it could expand when frozen and aid in the hairline cracks in your mortar.

I would repair the joints the best I could, adding a liquid latex (B-20) to the mortar mix. this will allow more flexibility. then I would seal the whole thing with a waterproofer like: "Gloss n' Guard" or "Weather Seal Siloxane"

this will keep the water out of your flagstone and joints.

Belden Brick and Supply Co. in Grand Rapids carries this stuff if you are interested. they may have more answers as well!

I have also tried filling the joints with sand & then tried using the dry mortar method.The joints look terrible with the mortar & now the flagstone surface are smeared with dried mortar ! I'm unsure of what to do next, I'm checking with concrete manufactures for possible options.