As far as I know, this issue has been around since 3.1. I even stopped upgrading at 3.0.4 for any sites where I knew the client would need to edit tabular data. For security reasons, it's time to upgrade these and I'd REALLY like this issue to be fixed.
To reiterate, the problem happens when creating paragraphs in a table cell. When I hit enter to create a new paragraph within a table cell, it looks fine. When I hit Update/Publish, when the page refreshes, WordPress converts that paragraph break into a single line break. If I then click Update again, WordPress removes that linebreak entirely and the paragraphs are essentially merged.
I can also reproduce this behaviour without even clicking Update. If you just switch to HTML mode and then back to Visual mode, the same issue happens.
This is definitely a bug and I've created a bug report for it http://core.trac.wordpress.org/ticket/20943. Hopefully this will be attended to.