That's a very good point. I guess if possible it is best to try and make your "day job" contract or freelance work with more flexibility than employment. That way you can to some extent dictate how you work, i.e. you can make it fairly clear that you only work 9-5 and that work outside that would be charged for.
I have two great clients at the moment who I am doing contract web development work for and since they're also both startups it works quite well and I can contribute a lot in terms of startup experience as well as just development, and I think that is valued. I'm always aiming to do my best for them and help them move forward as fast as possible, but there is definitely a clear distinction between that work and my startup.