We had a similar problem. Whenever an edit was done to the job it would reschedule the job to run at the next scheduled time, effectively skipping a job.
This was fixed by updating to BE 11d build 7170. I think one of the hotfixes was part of the solution, but I don't have the documentation in front of me to remember which one. I applied hotfixes: 3, 4, 7, 8, 9, and 12.