Hi Vinod.
We've found the success of Webi 'Export To' and 'Save As' vary system to system. The variables are enterprise security settings, browser security settngs & browser compatabilies. BOBJ 3.1 is a 5 year old technology now - as time moves on there is even less we can control.
For PDFs we train our users to click on View --> PDF to have Webi create the PDF in the Webi Viewer interface. From there, we have the users use the PDF Viewer's 'Save As' capability. This eliminates all random issues. We use Adobe for PDFs in our Enterprise.
HTH