You can try upgrading to a later sub-version of IE (IE 5.5.SP2 just came out) or you can try re-downloading the Microsoft JVM from http://windowsupdate.microsoft.com

I don't know why the Sun JVM would have interfered with IE, but I can tell you that IE is designed to NOT USE the real JVM, or any newer Java apps like Limewire. Basically, IE can only run Java 1.0 and 1.1 apps, while Limewire 1.6 is a Java 1.3 app.