It's tough to juggle both because you have to switch your mind from one thing to another. Not only this, but if you are working full-time and working on your company in your free time, you have little time left over to just relax. This caused me to burn out a couple of times a year.
Another concern of mine was that the company I was working for would try to claim ownership over my projects if they ever became successful. Even though the code bases were completely different (and so were the industries), I never wanted to take that chance.
I suppose I could have just put everything out there and told my former employer what I was working on, but this would have caused lots of problems for me.
I'm in a better place now and I've accomplished more in a week than in a month when I was trying to do both. I am also in a good position because I don't have a wife or kids. I realize that not everyone can do this.