Scanned to PDF, but pages are blank

Hardware
- iMac 2 GHz Intel Core 2 Duo
- Scanner Brother MFC-J6910DW
Software
- Mac OS X 10.7.2
Using Preferences>Print & Scan>Open Scanner; settings:
- Scan Mode: Document Feeder
- Kind: Black & White
- Resolution: 200dpi
- Size: A4/A3
- Duplex
- Format: PDF
- 'Combine into single document': checked
- Image Correction: None
When I scan and combine around >100 pages. I open the file in both Preview and Adobe Acrobat Pro 8 and discover that most of the pages, except for about 20 at the end of the document, are white with a grey PDF logo box in the middle.
Have I lost all that I have just scanned or are they still there but not showing?
Are my settings to blame, and if so, what should I change to ensure this does not happen for future scans (i.e 300dpi or higher?).

Just an update:
Forgot to say, I was saving the scans direct to a server.
I found that if I saved the scan to my computers desktop, I don't lose data no matter how large the file becomes.
I have a 1000+ document and all the pages are there with the above settings.
Also, my computer would request I update my brother software, automatically download, but never finish.
I was able to download the drivers manually here.
www.apple.com>support>downloads>(search 'brother'). Should be the first find.
However the direct link for the above is: http://support.apple.com/kb/DL894.
Hope that helps

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