OK re-install Avast
http://files.avast.com/iavs9x/avast_free_antivirus_setup.exe
http://files.avast.com/iavs9x/avast_pro_antivirus_setup.exe
http://files.avast.com/iavs9x/avast_internet_security_setup.exe
http://files.avast.com/iavs9x/avast_premier_antivirus_setup.exe
We did not actually touch any keyboard drivers so it may be a function of the way I disabled Avast
As to why the second drive is a problem I have no idea, it appears to be a quirk with windows, as about 30% of the non-booting cases are resolved by disconnecting the slave drive