Overcoming Java Security Warnings

Lately we have been experiencing about 3 or 4 Java Security Warnings every time a user logs into Remote Desktop. Sometimes the warning will come up in the background, leading most users to sit and stare at their screens because they don't realize the pop up is there.

Not all of our users are up to date with Java, but most are on 7.45 release. All users are using Internet Explorer 9.

So far we have tested a number of solutions found on Java's support page. We have tested changing Java's security settings, bringing it down to basically no security at all, I have tested changing the Mixed Code Protection, even testing bringing IE settings back to default and clearing all user data. All of the testing we have done leads us back to the same messages every time we try to log in.

Can anyone suggest any other options?
Zwolfe84Asked:
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jcimarronConnect With a Mentor Commented:
Zwolfe84--
I do not think you can turn those security messages off.  They are caused when Java regards the site as a security risk.  
http://www.experts-exchange.com/Programming/Languages/Java/Q_28285611.html

The messages each have a check box  option to close out if you signify you "accept the risk".
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CEHJCommented:
Not sure exactly which warnings you mean but you should probably begin by making sure all users are up to date. Outdated Java can lead to serious malware
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Zwolfe84Author Commented:
We leave specific versions of java running because a few websites that our users need access to don't update often enough and are incompatible with the newest version. We have these people in groups and know which users are and are not updated.
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CEHJCommented:
and are incompatible with the newest version.
How have they managed that? It's actually pretty unusual for software written for earlier versions of Java to have any problems at all running on later vms
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jcimarronCommented:
Zwolfe84 --
Here are more details on the reasons for the Java security messages.
http://www.java.com/en/download/help/appsecuritydialogs.xml
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LeeTutorretiredCommented:
I've requested that this question be deleted for the following reason:

Not enough information to confirm an answer.
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jcimarronCommented:
It is always hard  to "confirm" a negative answer.  In http:#a39666433 I posted that "I do not think you can turn those security messages off." by which I meant you cannot avoid having the messages appear.   I have seen no evidence to the contrary.  
See also the link I provided http://www.expertsexchange.com/Programming/Languages/Java/Q_28285611.html 
which  stated "but they (the messages) now are part of using Java in a browser" and "So changing Java's security level is not going to make the messages go away.".
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