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Unzip a copy of your epub and look inside the META-INF folder at the container.xml file.
It is an xml (text) file and can be opened in any text editor.
Look to see if there is more than one rootfile tag. Then make sure the rootfile full-path attribute properly points at what you think is your opf file. This path is relative from the root of the epub (where you see the mimetype and META-INF folder) and is not relative to the location of the container.xml file.
Note, epub3 epubs may have multiple opf files in them to hold multiple renditions of the ebook. That said, no one and nothing I know supports or uses that feature.
Hope this helps track down the issue.
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