For the Reference Checker to be able to read your document, it needs to be in plain text format (.txt), not in a binary format, like Microsoft Word's format (.doc). It's generally very simple to save your document in a plain text file. Here's how.
In Word or OpenOffice, just open your document, select File...Save As and in the dialog that pops up, where it says Save as type or Format, select Plain Text (*.txt) or Text Only or Plain Text. You may leave the name the same; the program will not overwrite your existing file, but will create a copy of it with the extension ".txt". (Make sure it gets the ".txt" extension.) If your file name is rather lengthy or strange, you may wish to head off problems by giving it a more normal name (like "econpaper.txt").
Note: Do not have the program insert line breaks! Don't choose an options like "Text Only with line breaks".
If there are special characters in your document, the program may ask you what encoding you would like to use. It's almost always safe to accept the defaults and just click OK. However, if you experience problems, I recommend that you use Unicode. The Unicode encoding UTF-8 is preferable to UTF-16, but both will work.
The program will warn you that some content will be lost upon conversion; this applies only to the plain text version you're creating, not to your original document. Click OK. Then close the document.
When you go to upload your document, just make sure to choose the .txt version of it. That's it.
Note about OpenOffice: When you save your document as plain text, you may lose any footnotes in the document.
In TextEdit, it takes two steps to convert your document. First, select Format...Make Plain Text. Then select File...Save As and choose Unicode (UTF-8) (preferably). Allow the program to give the file a ".txt" extension. That's it.
If you use a different program to create your documents, I would very much appreciate it if you would write up some instructions for your program like those above and send them to me so I can add them.
In converting your document to plain text, you will lose most of your formatting and some structure, for example in tables. However, this very rarely has an impact on citations. And of course, no data in images can be analyzed, but that is usually not an issue either.
The Reference Checker is smart enough to find your bibliography and distinguish it from appendices and footnotes/endnotes, so you don't have to worry about the structure of the document.
Note that this is a new window; your settings remain unchanged in the other window. You may close this window if you like.