I have an issue like this, too. It might be the same issue you're having (or at least related).
If you ever click into a tool window, then you can't use a keyboard shortcut immediately afterwards. You have to click back onto the main window first, then you can use shortcuts again.
This behavior wouldn't really be a major issue to me, except that I often use the eyedropper tool, grab a color, then adjust the color in the colors window. But then, when I click back onto the canvas to be able to use shortcuts again, the eyedropper grabs a new color, overwriting the color I just fine-tuned.