The most common reason for this is that by default watermarks are displayed in the background, behind the document's content. In most cases this is not a problem as the content of most documents is largely transparent. However this is not the case for PowerPoint presentations or scanned content.
The solution is to change the z-order of the watermark to a positive value to make sure it is displayed in front of the content. When using the Web Services interface this is a simple matter of settings the appropriate property. However, when using the SharePoint User interface (watermark on open/update), you may need to switch to our XML based watermarking syntax when using a software version older than 10.0. For workflows, and newer versions of our software, you can change the placement of the watermark by changing the appropriate option from 'Background' to 'Foreground'.
A simple example is displayed below:
Alternatively it may be possible that the font size is set too large for the watermark's dimensions, which may cause textual content to wrap into oblivion. Solve this by decreasing the size of the font, increasing the width and height of the watermark, or changing the wordWrap attribute (None, Character, Word or WordOnly).
Another possibility, although very rare, is that PDF files may have been opened before watermarks were enabled and cached in SharePoint's Blob cache or other caching solutions. Please clear the cache to resolve any problems.
When using our real-time watermark facility, e.g. 'Watermark on Open', then you have to make sure the Automatic PDF Processor is enabled at the Web Application level and configured at the Document Library Level (not just the Site Settings level).
Finally, if the watermark is set to 'Print only' (Available from version 10.0 of the PDF Converter) then the watermark will not be displayed unless the PDF is printed.