Sorry to hear you are having issues.
If an instance of Emote is present when you save your Logic session, then the H9000’s state (all effects, routing, settings, etc.) will be saved as part of that Logic session. This is a not a file you can access from a folder on your computer, it is only accessible using the state restore pop-up. This is different than saving a Session on the H9000. In Emote, if you chose Session > Save, this will save the Session file to a location on your computer. If you choose Session > Save to H9000, this will save the data the the H9000.
The Session always displaying “Default Session” is a known bug, and we’re looking into this. The important thing should be that the correct data is loaded, and from my testing, the state recall or manual Session loading always works correctly, but I understand that this is confusing.
The yellow square indicates that a Scene is pending, and has not yet been loaded. For example, if you use a CC to scroll through the Scenes, the square will be yellow until you load a Scene, then it will turn green. When a Scene Map is first loaded, the Scene should be displayed yellow since it has not yet been activated.
The lockups are not expected. If you can please email firstname.lastname@example.org and provide a Session that includes the Scenes you are having issues with, along with some steps to reproduce the issue, we can look into this for you.