This, unfortunately, is due to Micro$oft's war with Sun. Microsoft don't like other people having any control of the internet (or anything else). This means that M$ are frequently incompatible with the standard for Java laid down by Sun.

It may be possible to run both versions of Java - you will have to modify the shortcuts of the programs that use Java to use the appropriate version - I haven't done this so can't really give advice on how easy it is.

Mark