We are not aware of any conflicts with Microsoft Updates. I have seen some documentation on Sun's web site regarding the files that you mentioned were listed as damaged, and they say that they are not a problem. I don't remember precisely where the Sun documentation is, but it is available in the JRE installation documentation at www.java.sun.com.

This is, however, the result of the Sun's own installer that LimeWire launches, so we are not as intimately familiar with their setup. There are no conflicts that I am aware of, however.