Pdf to pdf convert - only small area of original pdf saved as new pdf

I got this app at the suggestion of the internet fax company I use.  I called because people receiving my faxes (that were scanned to my computer. saved as pdfs and faxed through email) could barely read the fax even though the pdf file I made was crystal clear.  She suggested the files were too large and using this app could make the files smaller and easier to transmit as a fax.  I tried converting a two-page pdf that I had scanned and the file that resulted showed only one very small area of the original document as the entire now one-page pdf.  I could not find any information in the help section or faq about this.  Any suggestions?