Is EndNote causing word counts in Word to disagree?

Over the last few months, some of my coworkers and I have noticed that sometimes, when we check the word count in a document or a selected portion of a Word document, the word count that appears on the status bar in the bottom left corner does not agree with the word count we get when we click the Word Count button in the Review tab. 

The couple of relevant hits I got when I Googled this problem suggested that it has something to do with EndNote. If that’s the case, is there anything to be done about it? We use EndNote in the vast majority of our documents, and although the problem seems to be infrequent, it could potentially cause a major problem when we’re dealing with a tight word limit.

We use Word 2010, EndNote X6, and Windows 8 (although we first noticed the problem when we were still using Windows 7).

Thank you.

Refer to this thread.

 

Also note that the word count may fluctuate if MS Word’s “include textboxes, footnotes, and endnotes” option is deselected (see attached image). Click the box to activate the option.

 
include textboxes, footnotes, and endnotes.gif

The explanation given in the other thread seems plausible except that it doesn’t explain why this problem only seems to come up in certain documents. I’ve experimented with a few different documents and couldn’t make the word counts disagree the way the have in some other documents I’ve worked with. Also, checking the “include textboxes, footnotes, and endnotes” box made no difference.

It’s really the sporadic nature of this problem that makes it a bit scary, because it’s easy to forget that the on-screen word count may not be reliable. You could end up cutting hundreds of words from a document to meet a word limit, only to discover later (perhaps too late) that you didn’t need to cut them.