If I understand, this error is occurring when you are importing the certificate into the SmarterMail service. If not, please clarify. Here are some things to check:
Make sure your system time is correct and synchronizing with a valid time source. It seems unlikely, but if the system time is wrong, the system may think the certificate is expired or not-yet-valid.
Open the certificate from within MMC. On the initial tab, it should indicate that the certificate has a private key. If not, you have found your problem. Next, go to the certification path tab. Click on each certificate in the path and verify that it says "Certificate is OK". If not, you need to fix the problem certificate or install the missing root certificate.
Finally, re-export the certificate, including the entire certificate chain and the private key. The server (in this case SmarterMail) is supposed to send the identity certificate and any intermediate certificates but not the root certificate. If the intermediate certificate is missing, this will probably prevent the import. I don't think the unwanted root certificate will be a problem. Removing the root certificate requires installing OpenSSL somewhere and doing some scripting to convert file formats. I can provide some sample code, but I don't think the root certificate is the problem.
Finally, re-attempt the import. I have not used LetsEncrypt, but I have used SSL/TLS on my ports, without difficulty, since we started using SmarterMail in late 2013. So I don't think it is a bug in their product. If LetsEncrypt is getting a valid certificate into MMC, you should be able to get it into your port definitions (assuming the port definitions have SSL/TLS enabled).
Hope this helps.