Rocky,
You’re using the milestone builds, I cannot recall at the moment if these problems were fixed and released.
Fortunately, you can go to Preferences > MyEclipse > Database Explorer > ER – Designer (where you will notice that all the colors are black – there is something messed up with 3.1 and default values)
Just change the colors to whatever you’d like and you’re home free.
Let me know if you run into any further problems,
Brian.