"and appears to be due to the Intellipanel shutting the peripherals' power off before the ext hard drive can power down."
Since the way you normally power down an external hard drive is by shutting the power off - I can't see any reason why this would matter.
A solution to any problem with an external drive shutdown might be to disconnect (the USB?)and power off the external drive first - use the "Safely Remove Hardware" icon in the system tray.
What exactly is "a shut down conflict on the PC which gets flagged up on Widows Start menu".
"A secondary problem ....opens directly on Windows XP"
In what way is that a problem?