I ran into this problem recently on our Citrix environment and it really perplexed me. We install Java via Enteo, We use the msi version of the java installation and we noticed that the java console was missing from internet explorer! At first i thought it was due to installing ie7 later in the script but it turns out the MSI does not install the IE addon by default!

If you are wondering how to get an msi for java (Suns website only provides an .exe) look here: Link

The command neccessary to install java and include the IE addon is below:

java.msi  IEXPLORER=1

The full command we use is:

msiexec /i java.msi /LV C:JAVA.LOG /QB REBOOT=supress IEXPLORER=1

This will install Java write a log to c:java.log and repress a reboot if neccessary.

Below are the rest of the undocumented switches, might save you some time

IEXPLORER=1 indicates that the JRE should be registered with the Internet Explorer browser
NETSCAPE6=1 indicates that the JRE should be registered with Netscape 6 or later browsers
MOZILLA=1 indicates that the JRE should be registered with Mozilla 1.1 and later browsers
INSTALLDIR specifies the drive and path of the installation
REBOOT=Suppress indicates that if locked files are encountered the computer should not be rebooted
JAVAUPDATE=1 indicates that Java Update feature is enabled