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I can't believe I didn't notice for months, but the signatures are not being trusted by Windows. If I sign the executable with signtool using the same certificate, the signature is trusted, so it's not the certificate to blame. The only difference I can find between the two is "digest encryption algorithm" is sha256ECDSA with osslsigncode, and ECC with signtool.
My signing command is:
osslsigncode.exe sign -pkcs11module "C:\Program Files\Yubico\Yubico PIV Tool\bin\libykcs11.dll" -pkcs11engine "%script_path%\pkcs11.dll" -pass "%pass%" -ts "http://timestamp.sectigo.com" -key "pkcs11:id=%%01" -certs "%script_path%\certificate.crt" -n "%name%" -i "%url%" -in "%in_file%" -out "%out_file%" -nolegacy
I've tried adding-h sha256 and different -n values, but haven't found anything that works. osslsigncode reports success and Windows shows a signature added. But it's not actually trusted.
I'm not sure what else to look at, but that digest encryption algorithm difference is standing out as the most likely problem.
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