This can happen if the IDE's "Window: Title Bar Style" advanced setting is changed to the "custom" setting. Obviously the setting should not just change randomly without action from the user, so this is likely caused by a bug in Arduino IDE. As a possible workaround, I can provide instructions for changing the setting back to the normal state:
Press the Ctrl+Shift+P keyboard shortcut to open the "Command Palette".
A menu will appear on the editor toolbar:
Select the "Preferences: Open Settings (UI)" command from the menu. ⓘ You can scroll down through the list of commands to find it or type the name in the field.
A "Settings" tab will open in the Arduino IDE main panel.
Type window.titleBarStyle in the "Search Settings" field of the "Preferences" tab.
Select "native" from the menu under the "Window: Title Bar Style" setting entry.
The "Restart" dialog will open.
Click the "RESTART" button in the dialog.
The Arduino IDE window will reload.
Close the Settings tab by clicking its X icon.
The IDE should now be back to the normal functional design with separate title and menu bars.
The Arduino IDE developers are tracking this bug here:
If you have a GitHub account, you can subscribe to that thread to get notifications of any new developments related to this subject:
Please only comment on the GitHub issue thread if you have new technical information that will assist with the resolution. General discussion and support requests are always welcome here on the Arduino Forum.
On my machine, where Arduino IDE works perfectly and I never have this problem with the title bar, I see the same thing. The "custom" option is marked as default, but the "native' option is actually selected by default.
I guess there is a good chance that the problem you are encountering is related to Arduino IDE fighting with Theia over the default value of the setting. Maybe there is some sort of a concurrency problem which causes the issue to happen only intermittently and only for a small subset of users.