Z170 OC Formula CPU custom fan speed not working

Decided to try out some ASRock boards for my experimental builds; I admin a university department so I'm always building something.  This time it's a Z170 OC Formula, BIOS 1.50, 6700K (not overclocked) with a Silverstone TD03 closed-loop liquid cooler and other random stuff I'll list at the end in the off chance it matters.

I would like to have as few spinning fans as possible while the machine is idle, which will be the state most of the time.  The cooler with just the pump running is capable of keeping the CPU cool when idling without any air moving over the radiator.  I have all fan headers except the one powering the pump configured with custom profiles with 0% fan speed below 50C, but I'm simply not able to find a configuration where all of  the fans stop spinning, and in some cases the fan behavior seems to change randomly on reboot.  I'm just doing testing in the BIOS with no installed OS.  (I know the fan speeds chosen in the BIOS only take effect after a reboot.)

Chassis fans 1 and 2 appear to power down as desired.  The pump is on chassis fan 3 and of course it's set to full speed.  The two fans from the cooler are on the two CPU fan headers, and nothing I can do will get them to spin down below 50% consistently, which appears identical to the speed selected by the "silent" fan mode.  A couple of times they've worked according to the speeds I've set, but most of the time they won't.  I swapped things around so that everything but the pump was connected to chassis fan headers, but then I couldn't get chassis fan 4 to spin down below 50%.

Is there any way to get all of the fans to obey the custom settings I've chosen and run at 0% speed below a threshold CPU temperature? 

Most of this won't matter, but just in case: Z170 OC Formula (BIOS 1.50), i7-6700K, Silverstone TD03 cooler, 64GB RAM (whatever Corsair DIMMs Newegg managed to have in stock), 3x Samsung 512GB M.2 SSDs, 2x 256GB Intel enterprise SSDs for booting, 2x EVGA GTX980 Ti Classified, Corsair AX1500i  PS, Silverstone FT05 case.  I think that's everything I've crammed in there so far.

Thanks for your reply.

Yeah, I should have mentioned the nature of the fans.  The two "CPU fans" (the ones attached to the radiator) are both 4-pin PWM fans.  The two chassis fans (the 180mm "air penetrators") are 3-pin.  They all do change speed.  There's a significant difference between "Silent" and "Full Speed", for example.

I understand that different fans require different voltages and that the percentages don't map linearly to any particular fan speed but I'd expect that the fans would at least stop if I specify 0%.  Unfortunately the custom speed settings appear to be ignored completely.  I do suppose this could be the fans, except that with some random arrangement of fans to fan headers I've actually gotten one of the CPU fans to regulate as expected.  It's pretty obvious in that case if the speed percentage is set too low to start the fan, since it "bumps" without actually spinning up.  But adjusting things so that the fans actually start is not the problem, since I can't get them to actually stop reliably.

I don't need to do this kind of thing often, but the last "fancy" machine I built had the previous generation of Asus Maximus Impact ITX board and it will stop all of the fans completely when the machine is idle.  That does, however, use a different cooler (with different fans, of course).  I'll grab some other 120mm fans from the pile (which will probably be 3-pin) and see if they make any difference at all.

I don't generally run windows on these but we have a site license so I can drop 10 on there and play with the utilities.

And yeah, it's a fun experimental machine.  Usually we use Asus boards (have about 150 of them around, mostly ITX or thin-ITX) but I've tried two ASRock boards so far and have been pleasantly surprised.  I do wish there was a Z170 ITX board without WIFI, though.  The H170 boards have no DisplayPort, so if you want that the price goes from ~$90 ( H170M-ITX/DL) to $130 (Z170M-ITX/ac).  Makes a difference when you're buying fifty.

I'm just using the plain customization entry, but the FanTastic thing displays the same curves.

I have rearranged the fans somewhat and found that if I attach one of the CPU fans to the CHA_FAN3 connector, it will obey the settings I set (which means the fan doesn't spin until it exceeds the set T1 threshold).  Connecting the same fan to CHA_FAN4 and configuring exactly the same settings for the fan curves in the BIOS results in the fan running identically to having it set in "Silent" mode.

I really think the BIOS is completely ignoring the customization settings in some cases.  

Yes, the M.2 sticks are SM951s.  Was planning to RAID0 all three of them.  I have a couple of Intel Pro 2500 SSDs for the boot drive, though they have to go on the secondary controller along with the optical drive that I put in there for some reason.  Linux won't care, of course, as it never needs BIOS RAID.  And it's just for the OS anyway.