Well, that's what I'm saying. It's not a reliable method of adding files to your CD. Sometimes it works, sometimes it doesn't. The automated addition of files to your existing image is always going to be a flawed process, unless someone builds a tool that will scan every feature and structure type used in the disc image and recompile the image with the same attributes.
To my knowledge, such a program doesn't exist.
I don't think there's even another program that does what WinISO does, this is because the programmers know it's a flawed, risky procedure. Most programmers won't add a "this might work" feature to their software.