To follow up on this. I just updated to version 3.5 and I am having the same issue. The captions are are showing up next to images. In the visual end of WP the image and caption looks fine but in preview or publishing it shows up next to image.
I tried changing the code in text but it changes back. Here's the code in text.
[caption id="attachment_8241" align="alignright" width="200"]<img class="size-full wp-image-8241 " alt="Obesity is a disease - changes to come?" src="http://www.livablefutureblog.com/wp-content/uploads/2013/06/RS65_girl-apples.jpg" width="200" height="300" /> Obesity is a disease - changes to come?[/caption]
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