I have not tried yet... but I *think* if you go into your google calendar online and change the color through that it will update on the phone. I have not tried that yet, but the custom colors I use on google show up on my phone
Had the same problem. Found a review on here comparing WebOS to Android and they mentioned the same bug. They stated that if you picked a color from one of the bottom three row from the web interface for google calendar it would work.