Meant to come back and update this thread for future reference.
The problem I ran into with Automap not working was not a Cubase issue, but the fact that I was running Cubase as an administrator (not even sure why I did that but I set the desktop icon to run as admin, and because Automap was not running as admin it could not communicate... this is why it was working in other DAWs that I don't use as much).
I also ran into a few recent freezes/audio hiccups, and I remembered a recent discussion here about Focusrite Firewire interfaces (and pretty much every other high-bandwidth Firewire devices) requiring the TI chipset on the 1394 port. So, just to eliminate possibilities I plonked a dedicated Firewire card into the PC today and disabled the built-in VIA 1394 chipset on the mobo. Only time will tell if it solves the occasional freeze, as I have not had much chance to experiment since the upgrade. If you have a strong interest in knowing if it made a difference or not, check back with me in a couple of months for some reflective thoughts on the upgrade and so forth
