JBuilder will make changes to web.xml files. It's an IDE and when you add servlets (for example) it will add the necessary mappings to web.xml
Also, because JBuilder might not recognize or be aware of changes *you* make to the file, your changes may be overwritten. I haven't used JBuilder in a while, but this is not surprising behaviour for an IDE.
When you run a web application within JBuilder, it modifies the web.xml to add a special jsp running servlet that will let you debug jsp's. I don't know how to turn it off. It really isn't a problem if you always stop the running web app before editing web.xml. Jay