Ironically, what can happen if you have ammonia from biodegraded CYA, is that you end up with monochloramine in your pool. This is the same algaecide that you're trying to produce when you use "Yellow Out", "Mustard Master" or similar products.

Monochloramine is a VERY good algaecide, better than plain chlorine. The problem is that it's a fairly good people-cide! It doesn't actually kill people, but it will run them out the pool with burning eyes and itching or red skin!

Fortunately, it breaks down pretty quickly as you add MORE chlorine, but during the brief periods when it's present, it can do a number on the algae.