We contacted EndNote and they told us that Instant Formatting needs to be disabled whenever tracking changes is enabled. So far it has been working for me, but I have not tried this while collaborating with other authors, which is when I first noticed
the problem.
Having Instant Formatting turned off is no problem. I just have to hit Update Citations and Bibliography to see the proper formatting applied to new citations.
Here are the instructions for disabling Instant Formatting:
"To disable Instant Formatting in the current document:
EndNote X1 and later:
- Word 2002/2003/2004/2008/2011: From the Tools menu in Word, go to the EndNote submenu and select Format Bibliography or Bibliography Settings.
Word 2007/2010: On the EndNote tab, in the Bibliography group, click the bottom corner arrow.
2. Click the Instant Formatting tab.
3. Click Turn Off to toggle Instant Formatting. Click Cancel which will save changes to the Instant Formatting settings and not format the document.
Basically you can leave the instant formatting turned off until the very end when the document is in Final form NOT showing Markup. Then update the citations and bibliography. "