1) Probably you have not set correct flags for window you are using as a backgound to your DX fullscreen surface (so your maximized window still do not cover taskbar). IIRC it sould be something like WS_POPUP and without borders.
2) It's not recommended to use DirectInput for mouse and keyboard polling under WinXP and later. This is due to DiretInput is emulated on these OSes, so use standard windows input functions for this. DInput should be used only for special controllers (for example force feedback is only supported in DInput).