There’s not supposed to be anything in the software that automatically draws the bounding box. (Try plotting one or more of the example files to verify that.)
The most likely cause of this kind of thing is when you work with imported artwork, where you’ve exported a *white background* along with the artwork that you intend to plot. The white background can come in as a rectangle that the AxiDraw software assumes it is supposed to plot. You can usually ungroup the background and delete it within Inkscape, or (better) update your export settings from where you’re generating this to not create that background. If you continue to have trouble, you might let us know how you’re generating your artwork, or send a sample SVG to us by e-mail.
As a side note, you can also use the plot preview function to see what will plot, before expending ink and paper; see section 9.8 of the user guide.