Chain break-in? I've never done it, nor heard of it. You've got great quality rings and cogs, and a good chain. There is NO WAY you have 'stretched' your new chain. I'm guessing there is some minor play between the ring and crank (when loose) and it's not exactly centered, and this is giving you the tight/loose spots. How tight/loose would you run your chain if everything was perfect? Remember, loose is fast. The reason you don't notice any difference when rotating the crank 90* is because the chainring is the problem, not the chain.