Actually iTunes should show your embedded covers. It definitely supports JPEG files, I’m not sure about PNG. I don’t think it supports external images. What you could do is import one of your eBooks into iTunes, add the cover in there, and then compare it to the original file. This way you should be able to spot any differences.
To do this you first need to drag the eBook into iTunes, select it and then drag the image from the finder onto the cd cover preview screen in the left bottom in iTunes. If it’s not there you can activate it from the menu bar. In English it should be under the "view" tab. Alternatively, you can select the eBook and press Command + I to open the information panel, and then click on the tab on the far right labelled "Cover" (or something like that). Then drag and drop the image in there.
Afterwards, the cover is embedded in the ePub file and by right-clicking or control-clicking the eBook, you can view the file in the finder. From there it should be possible to compare it to the original file and determine why it didn’t show any cover art before.
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