Thanks for the answer steve..
We are using Designer 9.0. Using designer we created the XDP file. The PDF was generated using the forms service of Adoble LiveCycle ES 2.5. So I was facing issue in certifying PDF generated by forms service and not when PDF was created using the designer.
As a test we changed the default form properties of the XDP file from static to dynamic. Again PDF was created using the XDP file via forms service. When this PDF was certified, the error was no more occurring. So we were able to solve the issue by changing form properties of XDP file from static to dynamic