Watermarks not showing on files when batch processed?

Hello,
I am using acrobat pro 9. I am looking to watermark upto 2000 files at work, I have researched and gone through all of the steps to set up a watermarking script for the batch function.
However once the process is complete, the correct files appear in the correct folder but are totally unchaged...the watermarkings are set to be veiwable on screen and when printed.
I can watermark and successfully save files if I do them one at a time, it just all goes out the window when I try to batch them.
I am batching 3D imaged pdf's if that makes any difference (doubt it would as they watermark the same as 2d)
used this link to help create the watermark
http://www.pdfzone.com/c/a/Document-Management/Add-Watermarks-to-PDFs-with-Batch-Processin g/
Can anyone think why I am having this trouble? Is there a simple option I am not selecting etc?
Thanks
Ali.

Ok here is how I have created the batch wateramark:
Advanced > Document Processing > Batch Processing
NEW sequence > input name (3D wateramark)
Select Commands: Add x2 'Add watermark'
This is how I set up the first watermark;
Then the second;
Now watermarks are in place ,select '3D watermark' and 'run sequence'
Edit the options....
The files are then selected > OK.
Loading bar appears, and the process appears to run.
Files then appear in the correct specified folder but are not watermarked.
Thanks.

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