As soon as system boots the system starts shutdown process - no time to hit start frontend.

AMD Phenom 2 3ghz
8gb Ram
500gb Primary HDD
2tb Secondary HDD
Mythbuntu 12.04
Mythtv 0.26

My system has been using ACPI wakeup and shutdown for a long time with no problems, but as soon as I installed the 2tb hard drive this week problems have started. Now the system shutsdown before I have a chance to do anything (including get logs!).

The couple of things I have noticed that may be a clue?
I am now getting the mmio address already in use error on boot, which I never got before?
The shutdown doesn't appear to be "clean" as the boot option menu pops up when I boot now?

I'll keep trying to get the logs, any help would really be appreciated!