certutil -generateSSTFromWU roots.sst
Then open roots.sst (which defaults to viewing in certmgr) and it will show the whole lot. Or use certutil -syncWithWU to get all the certs individually.Alternatively: download http://ctldl.windowsupdate.com/msdownload/update/v3/static/t... [1], extract the authroot.stl file (which is in PKCS#7 format), use 'certutil -dump' to list all the subject key identifiers therein, and then download them from the same location as authrootstl.cab by appending ".crt" to the identifier.
Windows is not lying about anything, you just need to look in the right place.
Also, if you want to examine the CTL list that Windows is currently using - which should be identical to the one above unless it's brand new or there has been a problem downloading it - this will extract it from the registry:
powershell -Command "[IO.File]::WriteAllBytes('authroot-local.stl',(Get-ItemProperty -Path 'HKLM:\SOFTWARE\Microsoft\SystemCertificates\AuthRoot\AutoUpdate').EncodedCtl)"
Then use 'certinfo -dump' or whatever you like, it's exactly the same format as the downloaded authroot.stl. This is the same registry data that the OP's CTLInfo tool examines.[1] as specified in https://support.microsoft.com/en-us/kb/2677070