Hi,
I found it very annyoing, if you have the focus on tool window (like layers), then the standard key shortcuts do not work.
Example:
start paint.net click on the layers window to select the background layer (I know it's selected already as this is the only layer now, but just for to reproduce) press "ctrl++I" -> nothing happens. This is true for all shortcuts, not only Invert command. To workaround, you have to click back to the image (to move the focus to the main window), then you can use the keys.
This is very annyoing, for example you have 10 layers, and want to run some command on 5 layers, you select a layer, then click back to window, then press keyboard, then select layer, then again click back to main window,....
It is like this in all 4.0.x versions, including the latest 4.0.5
Thanks.