When using a custom logo with the additional property white.background=true in the color.properties file the white background with the logo overlays the Message History Window.
Without the option white.background=true the Logo is not overlaying the Message History Window.
An issue was fixed where the custom logo overlapped other dialog boxes.
Do not use the property white.background=true for custom logos
Update to a fix version listed below or a newer version if available.
Automic Web Interface (UI)
Automic Web Interface 12.1.2 - planned release date: 2018-05-23