Thanks for getting back. The truth is I have many questions regarding the issue! (sorry in advance for filling the forum with stuff that should go to MSI Support!)
So as for PWM, yes, and no. I have been testing with both pwm fans and 3pin, both seem to have the same problems in all the headers, (minus CPU 1).
N.B: All components are new and installed new into the system.
With regard to config, I hope it is a config problem as well, but I think it may be a little more that just a few settings not ticked if you know what I mean, which is why I wanted to see if anyone else had the same issue with the board!
With settings, I went into BIOS and on the most recent visit set "Set All to 100%", and then checked this using MSI command center software to check CPU 1, CPU 2, sys 1, 2, &3 headers are to max which they were.
If I plug in any fan into CPU 1 it will not spin. If I plug in my AIO pump, the light on the pump flickers, but in the mostly off kind of way. I suspect CPU1 header is damaged.
CPU 2 Header works (sort of) and has full PWM support, so I will be referring to that header with these numbers, so initially, I had an AIO hooked up, but it was idling at 60'C! (6700k non overclocked) so i swapped that with an intel stock cooler, so the pump may be faulty but I suspect not.
Now for RPMs.
the stock cooler stays at ~2000rpm with settings set to 100%. Now we all know how loud they are! well this isn't loud, which is what I meant by "slow", now if I unplug and replug it into the header, it ramps up to 3000rpm for ~2secs and ramps down, and stays down. That ramp up to 3000rpm is the noisy stock cooler at its best that we've all come to love!
Now with the (maybe faulty) AIO, in the same header, it will flicker between 0 and 1800rpm (yes plugged in correctly), then settle at 0rpm once left alone (the LED is solid on in this time, no flickering LED. this is what I believe was causing the high idle temps. This gives me the feeling that the MOBO isn't delivering enough power to each of the fan headers, as it seems unable to sustain the maximum or operation speeds.
This makes me think it may be a BIOS problem, but being such a new MOBO, there isn't one to update to! And since its a new mobo, there are currently no forum thread that I have found yet to check with!
if you've read this far you are AWESOME!