Well, the hub adapter connects to one mobo 4-pin port to get a PWM signal for its fans, and to a PSU Molex output to get power. The issue is that such a hub MUST have PWM signal to share. Your posts say that the only SYS_FAN port you have is supplying the rear 3-pin fan AND that the port is successfully controlling that fan's speed, causing it to change. The ONLY way to change the speed of a 3-pin fan is if the port it's connected to is operating on Voltage Control Mode as a 3-pin port. This means that the port is NOT a true 4-pin port operating in PWM Mode, and does NOT provide a PWM signal on its 4th pin! Thus, the hub adapter thing should NOT be able to control even 4-pin fans if it is plugged into that SYS_FAN port.
There are two ways to handle this, each not quite perfect, but good solutions anyway. Since you will have 4-pin fans all around, one way is to make sure you DO have a valid PWM signal to use from a true 4-pin mobo port operating in PWM Mode. The only port your mobo has like that is the CPU_FAN port. This would put all your fans under a control system based on the temperature measured inside the CPU chip. That is ideal for cooling the CPU itself. It is not quite ideal for cooling the rest of your case interior (a different sensor, mounted on the mobo, guides the SYS_FAN port), but after all, the heat generation by mobo components is closely related to overall system workload and hence to the CPU heating. So doing this is OK.
There are just five things you'll need to do right for this.
1. Get a hub adapter cable set that can handle all of your fans - I believe you have four, one for CPU cooling, two in the case front, and one at case rear. Here's one with 4 outputs:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423165&cm_re=4-pin_fan_adapter-_-12-423-165-_-Product
2. Plug its 4-pin female connector into your mobo's CPU_FAN port. This allows it to pick up a PWM signal that it can share to its four fans, and send back to the CPU_FAN port the speed signal of ONE of its four fans.
3. Plug its Molex connector (only has 2 of the "regular" 4 pins) into a mobo female 4-pin Molex output to give the fans a power source.
4. Plug your CPU cooler specifically into the only hub output connector that has all 4 pins in it. This ensures that the mobo CPU_FAN port and its failure monitoring functions DO see the actual speed of the CPU cooler.
5. Plug your other (3?) case fans into the other outputs of the hub. Now all 3 of these AND the CPU cooler will be under the control of the CPU_FAN port. You do not need to use the mobo SYS_FAN port for anything.
The other option is to keep the three case fans separate from the CPU cooling system. This would involve connecting two of the to the SYS_FAN port via a Y-splitter, and the third to a fixed DC suuply that is NOT under automatic control. It also might use a speed reducer adapter for that last one to make it slower and quieter. IF you prefer this option rather than the hub system above, post back for more details.