The quick answer is from the terminal run:

$ defaults write com.apple.Dashcode NSQuitAlwaysKeepsWindows -bool false

The issue goes away after doing the changes to defaults and opening and closing Dashcode twice.

Long Version

There is a bug in Dashcode 3.0.5 that seems to cause project corruption on opening a project. In my case elements of my design disappear. What should look like

opens looking like:

The issue goes away after doing the changes to defaults and opening and closing the app two times.