Out of preference, and disloyalty to M$ I use Sun Java.
Unfotunately I don't know what you particular problem is, but you can check options in Tools, Internet Options, Advanced tab - about half way down the check boxes for Browsing options is the Java stuff...This is in XP Pro, but I'm pretty sure its the same for other windows since its IE. With Sun Java, you'll also get a control panel option for Java as well...at least mine does. I've got the SDK version, but I think its the same for the standard edition.
Someone else on Forums probably has a better answer...