I have setup a keystore as follows:
keytool -genkey -alias tomcat -keyalg RSA -dname CN=<server FQDN>,OU="Company 
Name",O=" Company Name ",L=city,ST=province,C=CA \
-keystore /path/keystore -keypass phrase -storepass phrase

I then generated a CSR:
keytool -certreq -keyalg RSA -alias tomcat -file /path/certreq.csr -keystore 
/path/keystore

I signed the certificate on our Windows Server 2008 R2 CA Server:
certreq.exe -attrib "CertificateTemplate:WebServer" c:\data\certreq.csr 
c:\data\certreq.cer

I added the signed sert:
keytool -import -alias tomcat2 -keystore /path/keystore -trustcacerts -file 
/path/certreq.cer

Lastly I added the Base 64 encoded X.509 root ca from our active directory ca:
keytool -keystore /path/keystore -keyalg RSA -import -trustcacerts -alias 
cacert -file /path/root-ca.crt

This all completed w/o error, so I created the connector in the server.xml yet 
when
domain clients connect to the ssl site, they are prompted with warnings 
suggesting
the root cert is not trusted?

Any pointers where I erred?
Thanks!
jlc

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