I actually have the same exact settings checked and unchecked, but don't experience any Java problems.
You may want to check in IE>Tools>Internet Options>Security Tab
For the Internet zone, be sure that the Security level is set to "Medium" or below.
Click on Custom Level
If you have chosen to customize your security settings for the Internet zone, be sure that under the Java heading, "Java permissions" is not set to "Disable Java."
You will want to select one of the three safety levels instead.
Also be sure that under the Scripting heading, "Scripting of Java Applets" is set to "Enable" or "Prompt."
You may want to check in IE>Tools>Internet Options>Security Tab
For the Internet zone, be sure that the Security level is set to "Medium" or below.
Click on Custom Level
If you have chosen to customize your security settings for the Internet zone, be sure that under the Java heading, "Java permissions" is not set to "Disable Java."
You will want to select one of the three safety levels instead.
Also be sure that under the Scripting heading, "Scripting of Java Applets" is set to "Enable" or "Prompt."