I intended "-dpdf" and "-dpdfwrite" to give different results.
Using "-dpdf" will produce an 8.5x11in page with the figure inside the box defined by the paperposition property. With the current fltk backend, this doesn't work correctly. The only backend format/output available is 640x480 pt eps (GL2PS_EPS). Thus "-dpdf" currently produces an eps file. Once the backend supports GL2PS_PDF, then pdf output will be available.
At present, using "-pdfwrite" will produce output that is always 640x480 pts (it is cropped at the eps bbox). This approach can be used to produce figures for pdflatex.
In short, I think the m-file part is working correctly for the fltk backend, but the fltk backend only allows for eps output with a bbox of 640x480. If the selected devices requires an eps file (for conversion by gs, pstoedit, and fig2dev) then you'll get what you want, but it will always be 640x480 pts in size. If you ask for ps/pdf/tikz/svg, you'll get an eps file that is 640x480 pts in size.
Ben