I think the title is pretty self-explanatory. The newest version of Xbox 360 firmware comes with a feature that automatically shuts down your Xbox after a period of inactivity, which you can set yourself. If I'm downloading something big enough that it takes longer than my shut-off time, will the Xbox wait until it's done before powering down?
The 6 hour turn off won't stop downloads if you have "background downloads" turned on. This is accessed via the normal 360 settings on the right most "screen".
If its downloading the power light will continue to flash after you've powered the console off. Sometimes it might take a minute or two before it kicks into this mode after being powered off - I'm not sure why but my 360 does at least.