If the certificate you receive from your Root CA requires an Intermediate CA certificate (chain certificate), it needs to be imported into the server's certificate store in the following manner:
Launch MMC
Click File, Add/Remove Snapin
Click Add,...
AD Ports used by Cornerstone
TCP %localmachine%:microsoft-ds %localmachine%.srt:0 LISTENING 4
[System] - Directory Services
TCP %localmachine%:1045 %localmachine%.srt:0 LISTENING 416
[lsass.exe] - Local Security Authority Subsystem Service
TCP ...