Bea,
The Warning is just that: a Warning, and should not affect the output(it's not an Error). You'll get it if any objects are even a single pixel outside the layout.
That said, it's possible that the page number may be outside the printable area. You should see some blue lines delimiters on the page, and if your page counter is outside the lines, it's possible they might be getting truncated. You might need to move the box up a little to be included in the lines.
Hope that helps! If that doesn't, however, it would be easier if we could see the form, and therefore I would recomment that you open up a technical support issue.
Regards,
Raphaël Lalonde Lefebvre