The Acrobat crop feature is not a "true crop". It just pretends to remove the margins by inserting a command to tell Acrobat and Acrobat Reader to ignore the margins. Other PDF software can't interpret these commands. It's been a frustration of many. (You *can* use Acrobat do crop the margins in a much more complicated way: by selecting the part you want to keep, copying, and pasting as a new page, then deleting the original page. Very tedious process, especially since there no way to do all pages at once, as far as I know...)
With soPDF, to keep it it in portrait orientation and not divide the page, you just need to use one of the Fit Height or Fit Width options rahter than "Fix 2x..." options, as I mentioned in the other thread.
You might also try some of the other PDF cropping tools out there. Calibre comes with a command line tool called pdfmanipulate that can crop PDF margins. (It may be accessible through the GUI; not sure.) The LaTeX bundle comes with one called pdfcrop. For a more radical solution, take a look at
PaperCrop.