Some of your problem can occur because in Windows case generally doesn't matter, but in epubs it does. Your problem could be a simple as Style, versus style, or an extra space in a file name...good reason to make them one word.
Many readers will not validate the epub, but if it is submitted to a publisher it may well be validated causing headaches for your client. If it is an in-house publication it doesn't matter, but tracking down what it was could be useful for your education...if not for your sanity! (grin)