I'd speculate that something in the mobo VRM circuit has changed causing the CPU to receive higher voltage than indicated. This would acct. for all of the issues that you've experienced. As long as it works fine I'd use it as is because Gigabyte's tech support is terrible IME. If the same situation occurs again with overheating you may be forced to warranty the mobo.
Building a reliable PC involves more than just assembling the parts. You need to be able to configure all of the BIOS settings appropriately. This can be quite involved and frustrating as it can require a lot of trial and error with stress testing. It is however often the only means to get a 100% reliable PC.