We solved the issue with the password prompts. It was the domain controllers causing the issues. We solved it by setting up a load balancing solution with NetScaler over 6 different domain controllers.

However the "HTTP JVM: WARNING: CLFAD0251W: Requesting user authentication. HTTP Code: 401" still shows on the console.

We tried installing version 9.0.1.7 of Traveler and HF417 for Domino 9.0.1FP4 but still the same. The environment is working but we would like for the message to not show.

HTTP 401 is very general in nature. Even cancelling the credential prompt challenges can result to an HTTP 401. I would recommend that you open a PMR with the Domino Webserver team to help you set traces so that IBM can analyze what causes those errors. 

If you are running Traveler and the warning message appear, once your users do not have any issues authenticating with their devices you could choose to ignore the messages.

If you wish to halt the message from appearing you can complete the following steps.

Create two files in the xsp directory within your Domino server's program directory called bootstrap.properties and xsplog.properties

In the file bootstrap.properties enter the following text.and save the changes

#log groups enablement
log_configuration=xsp/xsplog.properties

# Log system out logdir=c:/<dominoprogram>/_xsplog
# This should be the path to the xsp directory under the Domino program directory and will be unique to each customer.
C:/IBM/Server/_xsplog

In the file xsplog.properties enter the following text and save the changes.
com.ibm.domino.xsp.bridge.http.manager.level=OFF

Restart Domino

Note: Changing the level to com.ibm.domino.xsp.bridge.http.manager.level=SEVERE, in the xsplog.properties file will also prevent the warning messages from appearing. 
 

http://www-01.ibm.com/support/docview.wss?uid=swg21969577

We're having a similar issue and error with our users who have Apple devices and have been setup for Traveler mail using the Exchange account type. They're no longer able to authenticate with the Traveler server from their devices and the CLFAD0251W error appears in the Domino console. One of the users states that this occurred after installing a recent OS update from Apple.