Re : converting v cut & paste, what you're happy with is best.
Do the books that are giving you 'problems' have anything in common - eg did they all come from LIT, does the font in the source differ, etc, etc.
Some things to try - if you've not already done so:
- There must be something in the DOCX XML that causes Calibre conversion to output <i class="calibre2">xxxxx</i> and something different that causes it to output <span class="text">xxxxx</span>.
If you can isolate a sample of each into 2 DOCX's, convert them to EPUB, and bundle the four files + your Word Template into a zip and post here, then I'll have a look and maybe Kovid and others will too.
- In one of the books that's giving you problems type a paragraph, I'd probably put it right at the beginning, make sure its Regular style, select a phrase and make it italics then save as DOCX and convert. If its OK in the EPUB then it must a paragraph formatting issue - if its not then its probably a document issue.
- Cut & paste a paragraph that has italics from a Good LIT/PDF book into a Bad DOCX, also copy Cut & paste a paragraph that has italics from a Good DOCX into a Bad DOCX - convert the Bad DOCX and look at the ePUB. And vice versa - ie Bad into Good. This may provide clues as to whether its a document issue or a paragraph issue.
I don't like inexplicable inconsistencies either?
BR