Hello mmclarke! Welcome to the Windows 7 Forums website!
Some software which is both 32-bit and 64-bit capable will sometimes install into both the "Program Files" and the "Programs Files (X86)" folders. Raxco's PerfectDisk does that and so does the Realtek HD Audio, FoxIt PDF software and so forth.
So check the "Programs Files" folder, which is the 64-bit or X64 programs folder and see if there isn't that occurring with your installation.
Don't try to get too worried about all this, some software just does that, and I believe it something to do with providing smoother compatibility.
Thrax or Digerati probably have the answers to this question that make more sense than my answer.