@dutchie1,
Well if you're up for a bit of sleuthing it's time to start poking around in the innards, to see what's actually going on
If you've correctly changed the cover to SVG-style, the internal html code for the cover page should look something similar to this:
where the
red numbers are the actual pixel width and height values of the cover jpg stored in your calibre library.
So the first step is to open one of your misbehaving epubs in the calibre Editor (highlight book in library and press T). Calibre's cover files are (usually) called titlepage.xhtml and will (usually) be the first item in the Text list (left-hand panel) with a little brown cover icon next to it. Double-click it and the html code for the cover will appear in the Code View panel.
How does yours compare to the sample code above?