Jobs are not running as scheduled

My company has just implemented 24 x 7 scheduler and added some 100 jobs to the scheduler, these jobs are a mix of batch files, vb scripts and JAL scripts. When checking the job status each morning we find the scheduler indicates the job has run but the associated log file for the job and the task it is scheduled to complete has not updated. I can select run now on the job and the job runs fine updating the associated log file and completing the task it is programed to do. Can someone please explain why the job does not run correctly when scheduled? I have the jobs split by folder with a queue per folder.

Do you run the scheduler as a Windows service or as a standalone application? If service, do you use the same user account for the service as your interactive account?
Do you refer to any networked files in the jobs that start, but don't run?
Do you see anything interesting reported in Windows event logs around the time your jobs didn't run correctly?

The scheduler runs as an application.
All batch files and scripts are located on a local data store.
No messages referring to the scheduler in the event viewer.

On further investigation into the issue, I have noticed the queue was set to 50, I have increased each queue to 250 and will monitor over the next few days.

I didn't mean messages in even logs from the scheduler. I meant "anything interesting", for example, security related events like access denied, etc...

Do your batch jobs write to any log files? Is there anything related?

By the way, because the job log indicates that jobs are starting and finishing, it cannot be related to the queue processing.