OK, Italo, vou realizar os testes aqui; muito obrigado.
-- EDIT --
Bom, ainda não foi feito o teste do serviço, mas ao testar a consulta de lotes ao invés do envio destes, também ocorre o mesmo problema:
É enviado este pedido de consulta:
<?xml version="1.0" encoding="UTF-8"?>
08694889000166
380
lR9gV0su1BGDKuGqbNCfF4Sy41Q=
eBNMjDLPKokn9/9M55TefDXiDNST2SWROMmgz5vzs4f7nBupMTDi/ZHIfKVl5D0wE6cJE1ygPsUw5IAK5Tr/HbDdMKPGd0bEcdKrxU7wwzhjC3/ONa7Jf6cV435oOWm4gTJl4i5Z5TCgDh87Av+g91WQDE7hCCnW50l/FEf95AA=
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
E a resposta é esta:
<?xml version="1.0" encoding="UTF-8"?>
false
1107
O CPF/CNPJ da assinatura da mensagem XML não corresponde ao CPF/CNPJ do Prestador de Serviços.
Como se pode ver, a consulta é bem mais simples, contendo somente o CNPJ do remetente e o número do lote, ou seja, não seria afetado pelo problema do serviço. Além disto, neste caso, foi utilizado especificamente um certificado de São Paulo, com o CNPJ correspondente. Ainda assim, ocorre o mesmo problema.