I knew that Microsoft had to call their ECMAScript implementation JScript, but it never dawned on me that Oracle is the current owner of the "JavaScript" trademark: http://tsdr.uspto.gov/#caseNumber=2416017&caseSearchType=US_... Between this and Oracle's ongoing lawsuit against Google for their use of Java in Android, I have a pretty low opinion of Oracle.
I always assumed it was because that was Microsoft's "embrace, extend, extinguish" era and they didn't want to use the name "Java" but did want to imply that it was compatible. Also at the time, pretty sure that Sun still owned Java?
Visual J++ on the other hand was because Sun sued them over a Java implementation which wasn't actually compatible with Java, and misuse of the trademark, and all that kind of thing, so Microsoft weren't allowed to call it Java anymore. This ultimately led to the development of C#, so it was probably for the good in the long term, apart from some of the bits they copied from Java in what was presumably an attempt to make it more a direct alternative.