HTTP Error 404.15 - Not Found
The request filtering module is configured to deny a request where the query string is too long.
So server denies our request because while enrol/requesting certificate, we need to send the CSR(certificate response)in query string, so length is big. Checking the CertSrv/mscep's Request Filtering/Max Query String(bytes) setting on that erroneous server was 2048. Increasing this size to 65536 solved the issue. Between by default when you install NDES, the limit would be 65536, but looks like not always the case to be. We can also directly edit the values in applicatioHost.config(C:\Windows\system32\inetsrv\config)