Well, I must admit that I had the exact same problem as everyone else when it came to cropping a PDF produced in Sketchup and printed with CutePDF.
It took many hours of head scratching to realise what was going on and it turns out that the culprit is CutePDF, not Govert's proggie.
The reason why it doesn't crop properly is clearly stated on Govert's page for his PDF Cropper:
Originally Posted by Govert
Note that it does not crop the white space from raster images
and what type of PDF does CutePDF produce? - a raster image.
This results in you not being able to crop anything less than the Sketchup viewing window, even though you select a page size that is larger than the window when printing.
Oh well, back to the drawing board (yet again).