motherboard battery???

You don't have to have SpeedFan installed, but it is a handy monitor to have. The fact that the problem wasn't effected by changing batteries suggests that the problem may be with the contacts instead. It is not always easy to determine by a visual inspection, but that is where I would start.
Get a strong light, and if necessary a magnifying glass (for weak eyes like mine), and make certain that there is NO gap between the contact and the battery. It may be possible to use some kind of non-conductive shim to force the contact toward the battery, if there is any doubt. The contact that I'm talking about is the upper one that locks the battery in place.

That was going to be my next question...which contact, lol. Do you mean the one that sort of makes its way round the outside of the battery? The battery has nothing on top of it, other than a small clip thing attached to a metal ring that goes round the outside - i assume this clip is to keep the battery in.

Yes, that clip is also a contact. Take something like a match, or something else (non-conductive) that is stiff enough to move that contact toward the battery. If there is any movement, then the contact may not be sufficient. You may need to remove the battery to be able to bend that contact toward the battery, but that bending would need to be done very carefully to prevent damage to the contact, or bending it so much that it interferes with placing the battery back into the socket.

Standard 2032 button-cell batteries tend to explode if one if you attempt to charge it. The motherboard has a diode to prevent the battery from charging.

Ok, so theyre not rechargeable lol. Ill see what happens when i get back tonight

Theres a new one in at the moment. Came with the board. Did have an old 1 from another board, i blamed the problem on that battery...i was wrong

Ivan the SoSo said:

Most motherboard batteries(at least all I have seen )are lithium, any attempt to recharge can result in fire, or explosion...so no recharging circuit....Have you done a BIOS update?

We got kinda derailed here....a bad BIOS flash or a corrupted one can make a checksum error.....a new Bios can also make the error since it's a different size from the old one......

I just asked if you done a BIOS update YES/NO....I wasn't going to suggest a BIOS update, why?...if the power blips, or something goes wrong it can(maybe) brick your motherboard...updating the BIOS can also void the warranty....

Next step clear the CMOS as suggested by Dwarf....look in the paperwork for the exact procedure.....Next try a different(new)battery, or test with a multi-meter....if all that comes out good.....bad CMOS chip on the motherboard....if it was a virus the problem would show up on reboot instead of being time dependent....

See the problem....The BIOS has been updated, now they have the perfect out to deny warranty replacement.

What is done is done...no need crying over spilt milk....check on the warranty, play dumb (BIOS what?)....maybe you can get a board without too much trouble