Hi Shanker,
were you changing the printer device in VF31 compared to the original printer that was assigned to the invoice output. we had sort of similar problem earlier, where the alignment was working fine in LOCL printer & another SAP printer 1, however some alignment issues & greyed out issues were seen on SAP printer 2 & this was solved more from the printer configuration side.
you can check the invoices assigned to the printer ( which is used in VF31) alone & try issuing them alone & check the alignment issue occuring there.
Regards
Ilango