Jim, you will find that fertigation systems of any type will mess up drip systems very fast. The water in the irrigation system will have to be as close to neutral as possible with as little total disolved solids as possible for fertigation to work with small diameter tubing.
The problem goes back to the exchange sites on the water and the fact that fertilizer doesn't disolve in water it becomes a colloid. With this occurring, the adhesion aspects of the water droplet are changed making the colloidal solution in effect "stick" to the small diameter tubing.
One possible aspect to pursue would be to lightly irrigate prior to and after the fertigation cycle to try and flush the micro tubing.
Good luck with it.