We've created this Forum Thread with some workarounds and advice to assist you in publishing you ebook.
EPUB Conversion: Configure Microsoft Word Settings
When preparing your manuscript for conversion to an eBook in EPUB file format, follow these steps to properly configure your Microsoft Word settings.
NOTE: The steps described below are specific to MS Word 2007 or later versions. If you are using an earlier version or a different word processing program, refer to your software’s Help files to complete these steps.
Save a Copy of Your File:
Open your document and click File > Save As. Give your document a new name, such as The Greatest Book Ever Backup Copy and save. Of course you will use your own book’s title, but you get the picture.
View Formatting Marks
Click the Paragraph (or Pilcrow) button to display all non-printing characters. When this option is selected, you can more easily locate and correct formatting issues such as extra tabs, spaces, and incorrect paragraph spacing.
Figure: Show Formatting Marks Button
Turn off Track Changes
Go to Review > Track Changes and set to Off. If previous changes or comments are displayed in your document, accept the edits and switch from Markup mode to Final.
Do Not Let Word “Fix It For You”
AutoCorrect and AutoFormat features make changes to your document based on changes you make to selected text. Deactivate these features so that they do not undo assigned formatting styles.