Issues Creating PDF's From AutoCAD

My company is working on standardizing how our AutoCAD drawings are created from AutoCAD. In the past each AutoCAD drawing has been printed to PDF using a third party PDF printer such as DocuPrinter or BlueBeam PDF Revu.
While those methods work, the PDF files that are created are very large, and they take a long time to produce. Our drawing packages consist of several hundred files and take a couple of hours to generate through those methods.
I am trying to use Acrobat 8.0 Professional to streamline the process, as well as increase the PDF qaulity, reduce file size, and reduce time to completion.
Acorbat seems to work great, but I have noticed the following issues. I was wondering if anyone else as seems and fixed these already.
1.) While doing Batch conversion of files to PDF within AutoCAD using the batch Convert method, every layout in each the DWG file is converted to PDF. The PDFmaker does not seem to care about my AutoCAD settings which determine which layouts to plot. Is there a way around this?
2.) Some content is missing on some drawings. On some drawings, lines and other conten is missing from the PDF. If I do a Print to Adobe PDF the content is present, but if I use the PDFmaker the content is missing.
3.) Random colors. If I use the PDFmaker, some elements on particular drawings are coming out in Either Cyan Blue or Red on the PDFs. The items are black in the original DWG files.
4. While doing a batch conversion, there is an option to save an XML file with all of your selections. You can reuse this XML file later. The XML file contains a setting that looks like you can specifiy which layouts to convert. Does anyone know the available options that can be used here?
All of my testing has been performed using Adobe Acrobat Professional 8.1.2 and AutoCAD 2007. I have also tested using AutoCAD 2009, but noticed a considerable amount of other issues.

Thanks for your interest Bill.
I did just what you suggested. The file gets created, and when I open it in Distiller, the errors showed (log file) are the following:
Start Time: Martes, 29 de Abril de 2008 at 13:24:45
Source: jojojo
Destination: C:\Documents and Settings\Edgar\Escritorio\jojojo.PDF
Adobe PDF Settings: C:\Documents and Settings\All Users\Datos de programa\Adobe\Adobe PDF\Settings\Standard.joboptions
%%[ Error: undefined; OffendingCommand: AFIANZADORA ]%%
%%[ Flushing: rest of job (to end-of-file) will be ignored ]%%
%%[ Warning: PostScript error. No PDF file produced. ] %%
Distill Time: 00 Hour(s) : 00 Minute(s) : 00.438 Second(s)
**** End of Job ****
Jojojo was the name of the file created by AdobePDF printer. The word AFIANZADORA happens to be the first text word in my document. It seems it does nothing from the beginning. Can you tell me what's happening with this information ?
And yes, I can print from any other windows application and a .pdf file is always created.

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