The starter solutions were not designed with compatibility with Instant Web Publishing in mind. I strongly recommend you check the scripts in it for web publishing compatibility. If a script run from a web browser hits an incompatible step, the script just halts on that step.
Not only will the layouts differ when you view them in your web browser. Each web browser may display the layout with small differences. You'll need to adjust the layout designs by resizing and repositioning objects on the layout. You may want to use one set of layouts for web browser and the original set for FileMaker Pro clients.