I went throught the same thing with my son. We switched from Saxon to Chalkdust for Agebra 1. After getting more than half way through the book, he still did not have a good grasp of the basics of algebra. Seems that was all toward the back of the text, which we never made it to. Factoring and other basics had not yet been introduced, but some more complicated concepts had. He's back doing Saxon Alg 1, and now seems to be learning the building blocks of Algebra.
Grace