As your probably aware - I think the main issue you have is with your CMOS being reset. If on start it has figured the disk to be different to when it was installed it may try look at the wrong sector/track for the master boot record and not find it - hence the apparent disappearance of your OS.
As for why the CMOS is going its a bit of a strange one, I would reseat the battery to make sure - also clean the contact points for the battery to make sure there is no oxidisation causing an intermittent connection. Only other things I can think of would be a short on the reset jumper (Unlikely but check for dust on jumpers etc) or there is a dry joint somewhere which could be near impossible to find and require a soldering iron to fix.
What I would say is record the settings in the bios for the disk and if it resets again make sure you have those same settings to make sure it finds the MBR correctly.