I agree with Sunlite. Since you believe that Calibre is causing your problems, don't use it. Load the HTML into Sigil and save as an epub and see if the results differ from Calibre. Sigil has its own quirks which are well known, but it adds virtually nothing to HTML compared to Word. You could try to work in Sigil directly, if you only want to create electronic documents. But you need to be comfortable with HTML to some degree.
You might check out (using Sigil) how big the graphics are and how complicated the various img statements are. When it doubt, save a copy, dig into it and strip out everything but the actual image itself. You might also check if there are overlapping <div> statements that are putting multiple styles on something that might be relatively simple.
If there is a stylesheet, go in and gut most of the contents and see where that gets you. Try a number of things not intended to produce a perfect copy but to see where your problems are coming from.
There is also a macro available for Open Office/Libre Office which creates EPUBs. Since the macro is free and the ...Offices are free, it might be worth playing with.
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