signature verification issue with crypt32.dll CryptMsgControl api

Question

We have an application which transfer EDI documents using AS2 protocol where When we send data to one of our business partner and try to verify the signature of the MDN that business partner return to us and we can`t verify the signature of the MDN that business partner return to us.

We are reading the certificate from windows certificate store using CertGetSubjectCertificateFromStore api and verifying the signature using the below code. error code return from the below code - CRYPT_E_SIGNER_NOT_FOUND

if (CryptMsgControl(m_hCryptMsg, 0, CMSG_CTRL_VERIFY_SIGNATURE, pRet->pCertInfo))
{
     bSigVerified = true;
     dwError = 0;
}
else
{
     dwError = GetLastError();
}

Same solution is working every other partners that we are transferring the files. we have check with partner but so far did not find any solution, I really appreciate if someone help here, let me know if need more information.