Maybe you've started using Windows 7 recently?
In Firefox go to Tools –> Options –> Applications . Then scroll down to PDF Document or Foxit Reader Document (or whatever your PDF files are named). Highlight, and then click on the dropdown menu (right pane), and click on Foxit Reader – Best Reader for Everyday Use. Now, every time you click a PDF link, it will open PDFs in Foxit Reader and ignore the plugin.