A family of Microsoft word processing software products for creating web, email, and print documents.
I have this exact problem with Word 2010, Endnote x5 and a document with complex chapters, cross references and endnotes.
After reading this I tried this:
Endnote tab on ribbon.
Click on arrow at Bibliography bottom right
Instant Formatting tab
Settings...
Uncheck Scan for temporary citations
Seems to be working so far :)
I had to uncheck the whole "Enable instant formatting...." option for the bug to dissapear, it was not enough to uncheck the "temporary citations" option (Office 2010, Endnote X5)