Originally Posted by Tango Mike
My chapter headings use the Heading 1 style in Word modified to format the text in bold and all caps
If it's not clear from the other posts, your problem is the "All caps" modification you made. Remove that modification, Check your headings, then save as Filtered HTML and you will be fine. The "All Caps" is hiding the fact that some titles are capitalized and some aren't.
(If this was obvious from the other posts, ignore this