You only time i flush is when i start to make water and flush the membrane itself (manual flush). If your not flushing your membrane and just letting the water that goes through your RODI system get flushed down the toilet, well, you are just wastinf water.
The increased tds you are seeing post sediment filter is just a flush of sediment that comes off the filter when water starts flowing.
You want pain? I go through 10-15 gallons of top off water a day and blow through an entire catridge of anion resin every 150 gallons of water.
Not so bad though, i just recharge it with lye. I have like 3 gallons of the stuff so only have to recharge twice a year.
But anyways... flush membrane a couple minutes and then make water.. o tds is o tds.