Uploading a PDF via Firefox, told the file is not a PDF

I know the way to fix this problem is by deleting or renaming mimetypes.rdf in my firefox profile. The only problem is that on several computers, the problem is repeatable. I have one user that has to delete or rename the mimetype.rdf file in her profile every day.
Yesterday I created a brand new firefox profile for the user and only imported her bookmarks. Nothing else. Today she was unable to upload a pdf to a website, she was told her file "wasn't a pdf." I deleted her mimetypes.rdf and we were able to upload the pdf.
Any idea what could cause this to repeat on the same pc even with a new firefox profile?
User has a Windows 7 64bit pc using Firefox 29.0.1. All Windows updates are current. Adobe Reader 11.

I am noticing that the "bad" file has a lot more entries than the good file for pdf. I can't get them side by side.
Good file
<RDF:Seq RDF:about="urn:mimetypes:root">
<RDF:li RDF:resource="urn:mimetype:application/pdf"/>
</RDF:Seq>
<RDF:Description RDF:about="urn:mimetype:application/pdf"
NC:value="application/pdf"
NC:editable="true"
NC:fileExtensions="pdf"
NC:description="Adobe Acrobat Document">
<NC:handlerProp RDF:resource="urn:mimetype:handler:application/pdf"/>
</RDF:Description>
<RDF:Description RDF:about="urn:mimetype:handler:application/pdf"
NC:alwaysAsk="true"
NC:saveToDisk="true">
<NC:externalApplication RDF:resource="urn:mimetype:externalApplication:application/pdf"/>
</RDF:Description>
Bad file
<NC:externalApplication RDF:resource="urn:mimetype:externalApplication:application/pdf"/>
</RDF:Description>
<RDF:Description RDF:about="urn:mimetype:application/pdf"
NC:fileExtensions="pdf"
NC:description="Adobe Acrobat Document"
NC:value="application/pdf"
NC:editable="true">
<NC:handlerProp RDF:resource="urn:mimetype:handler:application/pdf"/>
</RDF:Description>
<RDF:Seq RDF:about="urn:mimetypes:root">
<RDF:li RDF:resource="urn:mimetype:application/pdf"/>
<RDF:Description RDF:about="urn:mimetype:application/x-download"
NC:value="application/x-download"
NC:editable="true"
NC:fileExtensions="pdf"
NC:description="Adobe Acrobat Document">
<NC:handlerProp RDF:resource="urn:mimetype:handler:application/x-download"/>
</RDF:Description>
<RDF:Description RDF:about="urn:mimetype:handler:application/pdf"
NC:alwaysAsk="true"
NC:useSystemDefault="true"
NC:saveToDisk="false">
<NC:externalApplication RDF:resource="urn:mimetype:externalApplication:application/pdf"/>
</RDF:Description>

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