Dear Nick,
1) NSIS installer make no difference between 64 bit and 32 bit version and install in old directory on reinstall. Probably you have 32 bit version installed before.
So just be careful and change it to Program Files

When you do clean install, this would not happen.
2) I think if you would install in program files, instead of (x86) directory, problem would be fixed. The same if you do clean reinstall.
Here is
FAQ topic about this, but unfortunately archive mentioned does not have 64 bit MFC libraries inside. Would add new one soon.
Best regards,
Alex.