It sounds like the Instant Formatting feature may have become disabled in these documents. Without knowing the exact version of Word you’re working with, I will include a broad set of instructions that includes most of the recent versions of Microsoft Office:
Open one of the Word documents where you’re encountering this behavior.
2a. Word 2002/2003/2004/2008/2011: From the Tools menu in Word, go to the EndNote Web submenu and select Format Bibliography or Bibliography Settings.
2b. Word 2007/2010: On the EndNote Web tab, in the Bibliography group, click the bottom corner arrow.
Click the Instant Formatting tab.
4. Click Turn On to reenable Instant Formatting.
5. Click OK to format all citations and build the bibliography.
Please let me know if this helps.
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