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Okay, I'm not sure these ideas are of help, but it might point in the right direction...
1) I know that Windows (all versions as far as I know) consider digits in file names to be text, not numbers. But the way that you named the files should have automatically corrected for things.
2) The only other thing that comes to mind, which your list of files to include should have corrected, is that one of the original ebook formats (LRM? MOBI? Sorry, can't remember) allowed chapter files to be listed out of order, but it would display chapters in the correct order. However, when converting books, users would encounter the problem you're seeing. I think it was in the TOC or NCX file? Somwhere in it's files there is a listing and it doesn't list chapters as 001, 002, 003, etc but as 001, 019, 002, etc.
Sorry I cannot be of any more help.
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