No, you can't change the colour of the flashing animation in the task bar.
This is because the flashing background is defined in the currently selected
Windows visual style, which can depend from system to system. Actually, the background isn't a simple colour, it is a replacement image for the 'normal' task bar button background. Therefore, to change the colour of it, you'd have to change the visual style in run-time or something (which is almost impossible, given that you need a patched uxtheme.dll to apply non-signed styles) or draw the button yourself in some way. None of these methods are easy to implement or certain to work properly, so I recommend you to drop the idea of colouring the flashing background... unless someone else says otherwise.
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