Why can't I cleanly reboot my Amiga with Ctrl-Amiga-Amiga?

The Amiga has a hardware limitation that makes it impossible to delay a reset by more than ten seconds; this is much less time than a Linux system needs to properly shut down (which can be anywhere up to about a minute). It would be dangerous to try to flush the disk buffers during this brief time, so Linux doesn't even try. Use the Intel "three-finger salute" (Ctrl-Alt-Del) instead, or better yet use the "shutdown" command.