Welcome to the forum!
What is "the usual problem of fill and stroke"?
We'll know more when we can see the SVG file. But I'm guessing the "box" you're talking about is the page border. As Moini hinted, you may be right, and there may well be a mask (or clip) in the file. The new Objects dialog will be helpful in finding it. (Object menu > Objects)
What is the history of the file? Often we find objects or pages which are clipped, when the file has been converted from some other vector format. If that's the case, there could be many clipped or masked objects. If so, you could handle them all at once by select all, then release either clip or mask, whatever it is.