I have installed Aptana studio and you can see the icon is being displayed, very huge.
Is it a unity bug or just Aptana Studio bug ?
When running Aptana Studio 3, the icon in the Unity launcher is a grey square with a question mark. The icon is present in the Dash.
Using Aptana Studio 3 I queued a lot of new projects -> "upgrade existing folder as a new project" and closed a bunch of them afterwards.