Instant web publishing renders layouts differently to a desktop version, there are a number of reasons for this.
The best option (in my opinion) is to create specific 'more lightweight' layouts for the IWP version of your solution.
You can create a startup script which then goes to the correct layout depending if the user is accessing the solution via FM Pro or via the web.
As for the buttons, there are a number of script steps which are not compatible with instant web publishing, some will simply prevent a script from running, which may explain what you are seeing when you say no buttons work.
Within a script, you can select an option (lower left) to show compatibility with IWP.