These cause more of the "similar name but different program" confusions that occur all too frequently. [See also Messenger and Messenger and Other Confusing Program Names]
Java is the older of the two. Java was developed at Sun Microsystems in 1991, long before the World Wide Web took off.
Java is actually a full-fledged programming system that was designed so that programs could be easily written on one operating system (say, Linux) and then used with few, if any, changes on other operating systems (such as, Windows, Mac and Solaris).
VBScript is a Microsoft creation based on Visual Basic. It is unique to Internet Explorer — it doesn’t run on anything except IE. Fortunately, we do not see much VBScript any more except in Microsoft Excel.
Updating to a later version of IE (everyone should be running IE 8, but I know they’re not) will probably solve the issue.
By the way, I’ve never seen that message with Firefox!