Thanks @pjft , I think you're right and its a combination of me misremembering and also the larger fontsize on my nes/snes theme amplifying the problem to an extent.
I just checked my Megadrive build which uses a much older version of ES with a Raspberry pi 2 and a slower SD card with my Newgen theme (my new sd wont be running at full speed without overclocking anyway ).
The previews for that build are big in pixel dimensions but I managed to compress them quite well using pngoo so the filesize of each image ranges 100-200kb (originally they were 400-900KB) and even then enabling show FPS I can see the frame rate drop in the same way. I think because the fontsize for the list on that theme is smaller the occasional skipping just isn't as noticeable but is still there.
So basically I'm just noticing something that has been there from the beginning. And for anyone else who has the problem it's easily remedied by making sure you keep the preview image filesize as low as possible.
I did notice one other strange thing regarding framerate but I need to test more. The carousel on my new theme seems to run around 60fps on a rpi3 but occasionally when exiting out from a system the framerate drops to around 45ps and stays at that frame rate until going into another system and backing out again. Obviously doesn't affect things too much but just seemed odd.