This seems a little mis-leading to me, but when creating a new Job, the Save button does not actually save the job. You still have to Commit it. SqlNav does ask if you want to commit if you close, but, since I hardly ever use DML with SQLNav, I always say No to the commit question if it ever pop up (so I don’t accidently change something unintentionally).
On the other hand, this may be a separate problem, but if you go into the Job Manager, then edit a job, you don’t have to hit commit. It is saved by clicking OK on the PL/SQL window.