I was running into the same thing and finally got it to go through successfully. Windows - I think maybe notepad adds a bunch of ^M to the certificate files. I opened up the files in VI on a Linux machine and removed them from the files with :%s/^M//g and the way to input that is :%s/ ctrl+v then ctrl+m //g and write the file back. Once I cleared all those from the downloaded cert from my Microsoft CA the Inventory Service installed the SSL certs successfully...finally. Was driving me MAD!
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