I don't know..i could be wrong..but i have a feeling that you're been taking flax too long without balancing it with something else. It is mostly the flax's soluble and insoluble fiber (similar to bran & pectin) that is making you poop. But flax is also high in Omega-3 OIL..and in a very unbalanced ratio to Omega-6.
If you take flax seed oil for too long, it creates an LNA/LA (Omega3/Omega6) imbalance and can inhibit absorption of LNA. The opposite is also true. People who use flax seed oil by itself for long periods have experienced symptoms of dehydration like dry flakey skin, itching, etc. If indeed the flax is causing dehydration with resulting constipation..then what's the solution?
The Omega6:Omega3 ratio of flax oil is ~1:4. Balance the high Omega-3 flax with a high Omega-6 oil..such as hemp seed oil (Omega6:Omega3 ratio is ~3:1 to 4:1), pumpkin seed oil, or other suitable oil. That way, you can still reap the benefits of bowel regularity from the whole flax seed without drying yourself out. Ideal Omega6:Omega3 ratio should be between 1:1 to 4:1. You can easily calculate the amounts you get from the oils you're using..and adjust the amounts accordingly to arrive at a suitable ratio.
Remember..balance is very important.