I tried to export to PDF. The file took up the entire PDF page as opposed to beign 3.5X4.5 inches.
What is the page size as listed in Acrobat, what is the Page size in InDesign (as shown in File > Document Setup)
Two things come to mind - They are the same page size, but Acrobat is filling the viewing area (normal behavior) whereas the old file had the Initial View set to pahaps 100%.
Confirm that you exported from InDesign and did not Print to PDF (Page Scaling could be invoked from the print to)