There are two corrections needed for the commands in step #4 in the Import the Root CA Certificate and CRL into an Intermediate CA from a Batch File section:
The -f option should not be used for existing certificate stores. This is to avoid accidental creation of new certificate stores. If you are mistyping the certificate store and use the -f option, a new certificate store is created which becomes a dead store.
The CRL should be added to the intermediate certificate store.
The correct commands would look like the following:
for %C in ( FloppyDrive :\*.crt) do certutil –addstore Root %C for %C in ( FloppyDrive :\*.crl) do certutil –addstore CA %C