"Microsoft Java" could mean two things: the Microsoft JVM which was discontinued long ago after Sun successfully sued Microsoft, or it could be Visual J++ the programming language Microsoft supplied for that JVM. Neither are Java, though both resemble Java.
However, I felt that MS has twisted their IE somehow, to make some of the Java applets or application load faster with MS JVM, I mean some, might be developed using older version of Java, so far only limited to some site that I always visit.
I only want to install Sun JVM and JRE, I don't want to install MS JVM (though I have installed it a few months back due to incompatibility between IE and some websites), because you'll find it almost impossible to remove MS JVM from your machine, and by uninstalling using the tools provided by MS or third party will mess up your system, according to some IT techies. -.-" this doesn't sound good, does it?