Tax audit

Dear Sirs,

We are a firm and registered under societies act

We get audited our books of accounts. But our auditor had not filed our return electornically and not used digital signature.But under sec 44A whose books of accounts audited by CA  and   use digital signature.But our auditor said there is not necessary  of Digital Signature because we are society. First he said DS is must for everybody later says it is not necessary. and he filed our reurn manually after 30-9-2011. Is there any penalty be charged for late return or exp be disallowed.Please give suggestion in this regard

Thanks to all