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First, keep in mind that the Publish Online feature is labelled as "experimental technology" and is still in development.
>The images that don't partially originate from an old pdf created in an older version of ID.
How did you get them from the PDF to your current version of InDesign? Copying and pasting wouldn't be the best idea. A better way, if you have Acrobat Pro, would be to use the Edit PDF tool and in the Objects section of the panel, choose Edit Using to open the image(s) in Photoshop. You could save those as PSD files and properly place them into InDesign. (This description is for the current Acrobat DC version. It's slightly different in Acrobat Pro XI.)
Thank you Steve,
wasActually, I brought the whole layout of the old booklet into PS > Crop>SELECT ALL>COPY>CTRL N>CTRLV>CTRLSAVE (CTRL=COMMAND) then I simply PLACE them in ID works well and exports to PDF no prob. There must be some metadata that keeps them from displaying in the cloud-based site. That being said, later, there was a page that didn't display that actually originated as jpg's from my Nikon D90. (pics of business cards, cleaned up in PS then PLACED in ID )