Hi Javier,
The Integrity Eclipse Integration follows the Eclipse preferences for ignored resources, so to have the integration pick up these files, you need to remove *.class from the Team Ignored Resources. You can do this under: Window -> Preferences ->Team -> Ignored Resources, uncheck *.class.
Whether your view in Eclipse shows or doesn't show the .class files would be based on which views you're using in Eclipse, and how they are configured. I believe the Navigator view is the one most likely to show .class files by default, as opposed to the Package Explorer.
Does this help?
Kristina