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It doesn't sound like you are using the right option in the Modify ePub plugin. You need to tick "Insert or replace cover" to get whatever cover you have associated the book with in calibre (such as by using the Generate Cover plugin or downlaoding metadata) inserted at the front of the ePub.
If you instead just tick "Remove existing cover" it is going to remove whatever cover page is currently set, and the book will open at whatever page happens to be next. Which might be an image page of some kind, or it might be text, depends on what is inside each book.
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