Here is a project demonstrating the issue:
https://github.com/wetbadger/GodotMouseEnteredIssue
If you run the scene PartiesPane.tscn and click on the red or blue square icons, it will open a custom color picker window. Signals, such as mouseentered do not work on the ColorRect or Area2D. Neither does buttonup/down work if I change the ColorSquare.tscn to a Button node.
However, if it is run from the scene: BColorPickerButton.tscn, all signals are working.
What have I done to make the ColorSquares not work in one place, but work in another?
UPDATE: For some reason (and I have no idea why) changing Window from a Control to a Node2D fixes this.