After carrying out a clean installation of the PDF Converter for SharePoint, the Muhimbi.PDFConverter Feature is enabled by default on all Web Applications. As a result the basic Convert to PDF menu options are enabled on all Site Collections.
However, if an Administrator then enables this same Feature at the Site Collection level then all options are displayed twice.
If you wish to enable the PDF Conversion facilities only on a select number of Site Collections then please disable the Feature at the Web Application Level in Central Administration and enable it on the Site Collections of your choice.
For details about the various SharePoint Features that ship with the PDF Converter see section 2.2.3 in the Administration Guide.