[snowmaker]

As someone who's hired a lot of engineers at a startup, a very simple and yet highly effective thing you can do is to address this head-on in your cover letter. Just say what you said in your post: that you really loved working at a startup and specifically want to go back to one. That makes a big difference by telling me that a startup isn't your back-up plan if you don't get hired by a big company; it's your first choice.

Also, (and sorry to promote our own stuff) but you might look at workatastartup.com, a website we built to help engineers join YC startups. I'd be happy to look at your application and give you some feedback if it would be helpful.