So, your system has only two fans in total: the CPU cooler by Cooler Master plugged into the CPU_FAN header, and one rear exhaust fan by Noctua plugged into the H_AMP_FAN header. That's all, right?
The specs for those say their max speeds are 2000 RPM on the Cooler Master, and 1500 RPM on the Noctua. Where are you reading the actual speeds? In BIOS Setup, or using the ASUS utility AI Suite 3? What are those speeds?
As a quick check of function, try this to gather info. Open your case so you can watch those two fans closely immediately after start-up. Reboot your machine and watch what they do. The normal sequence at start-up is that all fans are started at full speed. AFTER a few seconds as the POST process completes and the system gets actual fan speed and temperature readings, each fan slows down to the slower speed required for a cool system. So, do BOTH your fans start fast and then slow down?
You report results you get when using BIOS Setup to observe and set options. Of course, you can use that only when your machine is not doing normal activities. To observe and set such things as fan cooling system while actually working, you need to be using the AI Suite 3 utility from your mobo's DVD disc. That set of tools (including Fan Xpert) is a Windows app you can run under normal Windows operations so you see information in real-world conditions. But NOTE this. IF you have that utility running it may well remember whatever settings it has and over-ride whatever you set in BIOS Setup so that the Fan Xpert settings take over while you are running normally. You should look in AI Suite 3 and Fan Xpert to see what settings have been made there and what the real fan speeds are under various conditions.
I think you have the correct settings figured out. In the BIOS Setup screen for QFan Control (mobo manual p. 3-7) for each of those fan headers the option at upper right should be PWM, and the PROFILE choice available below the graph should be Standard to start with - this is the pre-set automatic control that SHOULD adjust your fan speeds according to measured temperatures at the relevant sensors. When using Fan Xpert under AI Suite 3, you should have similar options set.