Adobe tells how to Flatten PDFs for faster printing!

PDF files can contain layered content if they are created from layered documents by using applications such as Adobe InDesign. As a result, a single page of the PDF file can contain different layers with different content. If you print a PDF that contains layered content, only the layer that is currently visible onscreen is printed. Acrobat Pro and Pro Extended let you specify which layer is visible and printable. Merge or flatten the layers in the PDF to determine if one of the layers is causing the printing problem.

Note: Merging or flattening layers can't be undone. For this procedure, use a copy of your PDF.

To determine which version of Acrobat you are using, choose Help > About Adobe Acrobat (Windows), or Acrobat > About Acrobat (Mac OS).

For Acrobat 8 Professional or later:

1. Make a backup copy of your PDF file by choosing File > Save As and giving the copy a new name.
   
2. Open the copy and choose Advanced > PDF Optimizer. If asked whether you want to save and continue, click Yes.
   
3. Select Discard User Data.
   
4. Select Discard Hidden Layer Content And Flatten Visible Layers, and then click OK.
   
5. When prompted, save the Optimized PDF with another new name.
   
6. Open the Layers panel (if the Layers panel is not visible, choose View > Navigation Panels > Layers). Click the Options pop-up menu, and then select either Merge Layers or Flatten Layers. Merged layers acquire the properties of the layer into which they are merged. Flattening layers discards any layer content that isn't visible onscreen. 
   
7. Save the PDF file and try to print it.

For Acrobat 7 Professional:

1. Make a backup copy of your PDF file.
   
2. Open the copy and choose Advanced > PDF Optimizer.
   
3. Click the Clean Up tab.
   
4. Select Remove Hidden Layers Content and Flatten Layers, and then click OK.
   
5. When prompted, save the Optimized PDF with another new name.
   
6. In the Layers panel, choose Options, and then select either Merge Layers or Flatten Layers. Merged layers acquire the properties of the layer into which they are merged. Flattening layers discards any layer content that isn't visible onscreen.
   
7. Save the PDF file and attempt to print it.