I had the problem, that when I put boxee in the startup folder, it loads the application after starting windows, but then the new Windows 7 taskbar gets in the foreground and I cannot control boxee with my remote control. I need to use the mouse and select the boxee application (so the taskbar disapears and the remote control works normally).
I found a simple trick which starts boxee with a little VBS script. Simply put this script in the autostart folder (instead of the boxee shortcut) and the problem is solved. It waits 3 seconds before it starts boxee. This is enough to get rid of the stupid taksbar effect. Worked for me... just in case you have the same problem ;-)