The certificate is fine and has correct SCTs in it. I think it's probably impossible for Let's Encrypt to issue a certificate that hasn't been logged - the order finalization should fail.
I think we have occasionally seen users report this problem with brand new certificates on some platforms. I have a theory that it happens when the system clock is slightly behind and the OS observes an SCT "from the future" (because SCTs are not backdated by an hour, like the certificate validity period is).
I think Chrome on Windows uses the operating system's native SSL validator. You could try clearing the SSL state and seeing whether that makes a difference with the certificate in question.