I had issues where a job seemingly stopped working even though it showed enabled and scheduled. I was able to track it back to a line of TSQL that was re-enabling the job if it was disabled. We have a notification job that is sending messages but when someone was working on areas that would cause notifications they would manually disable this job while it was being worked on. So we have a second job that was a "fail safe" that would check if the original job had been disabled for more than 30 minutes and if so it would re-enable it, but the problem was that it re-enabled it via an UPDATE to the sys.jobs table directly instead of using sp_update_job. Once we switched that command it solved the issue.