I've seen problems with impending HDD failure manifest themselves as a drive spinning up too slowly and not appearing in the BIOS on initial boot-up, only appearing after a hard reset.
I've also seen PSU problems manifest similarly, with HDDs taking longer than normal to spin-up and one or other (or both) not being detected in BIOS.
Both of these can affect the drive order in the OS, although granted it's usually because one is missing!
AFAIK, the CMOS battery is really only there to keep the RTC up to date - the BIOS code and data is all in flash or EEPROM nowadays.
SD