PDFE can't use the Foxit reader directly, so it must interface it through an embedded IE instance.
Because of this, Foxit must be configured to show PDFs embedded in IE, and this is what usually happens after installing Foxit, so something changed since you installed it, or you installed it with custom settings.
So, to try to fix it, start Foxit as stand alone, and if you are using Windows Vista or Windows 7 with UAC turned on, make sure you run it as administrator (just go to where you have the Foxit Reader .exe, right click it and select the "Run as Administrator" option).
- First make sure that in the Foxit Internet preferences, menu Tools>Preferences-Internet, the "Display PDF in Browser" option is set.
- Now check also if the menu "Help>Set to Default PDF Reader" option is checked.
Now start IE and try to open an online PDF (just google for "filetype:pdf" to get one). If Foxit is showing in IE, it will show in PDFE too.
Make also sure that in the PDFE preferences, menu Edit>Preferences, the Internal PDF Reader is set to the "Internet Explorer Default", option. In your case, because of what you described, it is already set.
If all this don't work, and you feel comfortable editing the Windows registry, just change in this key
HKEY_CLASSES_ROOT\MIME\Database\Content Type\application/pdf
the CLSID value to the Foxit reader CLSID
CLSID={14E8BBD8-1D1C-4D56-A4DA-D20B75EB814E}
Let me know if problem persist, and this time tell me what Windows you are using, and if it is 32 or 64 bits.
The Foxit Reader forums are also a good place to get assistance on this, because the only think you need really need to fix is to make Foxit to show in IE, when you open an online PDF with it. After that, will show also in PDFE.