If you're using the Windows GUI, there is an area where you can graphically select a box that will trim over multiple pages. This might help you avoid having to use the "autocrop" option, which doesn't always work quite right. See the attached screen shot.
The
autocrop option (-ac) also has a numerical setting which tells it how aggressive to be. You could try varying it. It depends on your document. If you could post a few sample pages that would help.