I faintly (& could be imagining it) remember a bug in the ISAPI for IIS a while back that corrupted either binary or large files (or both).
Can you try uploading your war file directly to Tomcat; instead of through IIS and the connector?
Also, if you want some small simple war files to
test with, I have a bunch on my own site:
http://simple.souther.us. SimpleServlet is a real small 'Hello, World'
servlet app.
They were all built with the 'jar' program that ships with the JDK.