If students are failing the entire class because of agenda checks, then the assignment is too heavily weighted. Grades are supposed to tell us how much the students actually know, not how well they cooperate. While participation grades and agenda checks can have their place, they should not have an enormous effect on student grades.

You can't really justify them failing for failing to record something in their agenda book because grade and passing and failure should be based on student's ability to master the standards, not whether or not they copy something in their agenda. The only thing I can think of is to call or email those parents who's students don't record and get them on board. More times parents have more effect on the things that their child does.

I would first have a conference with their parents and the administration. I would also make sure that the understand the importance of what you are asking. If they think it is just because you said so the will not be likely to complete it. If they are given he reasons as to why they are doing it they are more likely to complete the task. Also, have you used a reward/punishment for them besides a bad grade? Teach them how to write short hand or to paraphrase so it is a little less writing?

If I understand correctly, you are simply asking students to copy a list of topics into their agendas each week and then giving them a zero because they haven't done so. If that is the case, I would re-evaluate the purpose of asking them to such a task. Are they writing it down just so they remember what is being talked about in class? Are they writing them down so that their parents know what you are covering? You may want to implement something called a notebook check instead. My ninth grader, in his literature class, is evaluated each week on the quality of work in his notebook, not simply on whether he has written something down or not. The notebook includes his personally written notes from lectures and discussions that take place each day, homework assignments that have been completed as assigned, a reading log, and various responses to the texts that he is reading. It also includes bathroom passes that he has used in the class throughout the week, as those are traded in for extra credit at the end of the nine weeks. The notebook is a great learning tool for him, and it helps to keep him organized.

I really think positive reinforcement is the key. I've seen positive encouragement work well. Perhaps accountability,have a partner check their agenda. No, I won't have them fail, I would find positive things to encourage them.