Try scanning smaller batches. Does that work.
Scanning is a tricky process: You will need three different software systems to work together: The operating system, the scanner driver and the application, and then you also have the scanner hardware that needs to play with all the other parts. Unfortunately, based on my experience, scanning is even more unreliable than printing (where you have a similar situation), probably because a lot less people are using scanners than are using printers.
Even if you cannot make your scanner work with Acrobat, you can still use Acrobat's features to optimize your scanned document: Scan with the software that came with your scanner, either directly to PDF if there is such an option, or to TIFF images. Make sure that you select a reasonable scan resolution (e.g. 600dpi black&white or 300dpi grayscale or color). Once you have scanned your document, open Acrobat and import these scanned page. If you were able to scan directly to PDF, just open the PDF file. If you have a number of TIFF images, select File>Create>Combine... and select all your TIFF images in the correct order. Make sure that you click on the Options button and select "Large file size" and Single PDF.
Now that the document is in Acrobat, you can run Tools>Document Processing>Optimize Scanned PDF to apply the same processing steps that you could have applied when scanning directly into Acrobat.
This does not solve your problem with scanning simplex and then combining the two scans into a duplex document again. You would need JavaScript to do that.
Karl Heinz Kremer
PDF Acrobatics Without a Net
PDF Software Development, Training and More...
http://www.khkonsulting.com