Once you have set the brightness it should stay
and stuff should not disappear out of the dock.
On the second subject, I suspect that you are running something from a disk image which is unmounted, and is removed from the dock, when you reboot.
What browser is it that disappears.......Firefox?
When rebooting my iMac OSX 10.5.8 Leopard (a) a browser or application icon sometimes disappears from the dock and (b) the screen reverts to maximum brightness. Is it possible to (a) "lock" the dock so it appears as previous and (b) retain the preferred (lowest) screen brightness?