PDF's can be complex documents especially if they have forms with entered data on them. Many places will not accept these types of PDF's especially if they are being submitted for print and will usually ask you to flatten the PDF before submitting them. This is to prevent the loss of data on the PDF. Basically, flattening the PDF is putting it in a state which is ready for print and cannot be changed essentially converting everything in the PDF into an image.
We attempt to flatten all PDF's that enter our system, however the best result can be achieved if you flatten the PDF in the software you used to create it in the first place. This way you know the PDF will appear as you see it once it has been printed and avoid the possible loss of data fro your PDF forms.