Run Batch Jobs on a schedule

No, batch sequences are meant to be run by a person actually pushing the buttons. This is to deter Acrobat from being used as a server. However, you could write a custom plug-in to do this. Or you could automate acrobat a different way, for example, with a custom VB application that could be scheduled.

Or you could get a 3rd party program that is meant to be automated, like SWITCH from www.gradual.com or PDF Enhancer from www.apago.com

I'm good with VB, but I can't find anything in the adobe SDK where it talks about batches is there another reference that would be better?

There isn't. If you choose to go this route you'll need to essentially create you're own batch process. Opening the PDF files in Acrobat and using the IAC API to manipulate the documents, save, and close them.

If you already have the SDK docs then look through the Interapplication Communication Reference and the guide to find the PDF operations you want to perform.

This methodology takes a bit more work that creating a batch sequence, but it is infinately more controlable.