CPUID does make other programs besides CPU-Z you know, aber... HWMonitor to be more specific.
I'm not surprised that it isn't registering your fans correctly; mine never show up either on an MSI 790FX-GD70 board. Not sure why...
I don't really know what to say here, as I can't think of a single thing that's causing this problem other than a defective thermal probe in the CPU, and even then I think it would still register with something. Your board is a new(er) model, too, so it wouldn't be CPU incompatibility, either.
All I can say is, if you can get it to work some how, then feel free to share it with us. Sorry about my lack of helpfulness.