Most likely the problem is that ImageMagick is having the PDF rendered to a bitmap by Ghostscript, and then exporting the bitmap wrapped up in a PDF file. Without seeing the original I can't say for sure, but if the original contained JPEG images, then most likely you are ending up with JPEG being applied twice, or simply rendering at all is causing the problem.
Your best bet is going to be to use a tool which can simply apply a CropBox to the page(s). You can do this with Ghostscript, for example (which may also modify the PDF in other ways, including the double JPEG quantisation, so beware).
gs -sDEVICE=pdfwrite \
-sOutputFile=cropped.pdf \
-dBATCH -dNOPAUSE \
-c "<</ColorImageFilter /FlateEncode>> setdistillerparams" \
-f <input.pdf> \
-c "[ /CropBox [ 0 0 100 100] /PAGES pdfmark" \
-f
The first section between -c
and -f
tells the pdfwrite device to use FlateEncode for colour images, the default is JPEG, using Flate will ensure you don't get quantisation applied twice.
The second section between -c
and -f
tells the pdfwrite device to write a CropBox to the file and to make it 0,0 to 100,100. The units are the usual units in PDF; 1/72 inch, you can use fractional values.
I'm sure there are other tools which will do this, possible even more easily.