I think I can see now, but please check this for misunderstanding.
1. The case has two front RGB fans pre-mounted and now connected to your mobo's SYS_FAN5 header. I presume there is a Splitter involved for that. I presume these fans suck air INTO the case - correct?
2. The Kraken X52 radiator is mounted right behind those two FRONT fans, and still has the two NZXT fans supplied with it mounted on the rad. I hope the NZXT fans are mounted so they pull air INTO the case. That is, air flow is from front outside, though the RGB fans, then through the rad, then through the NZXT fans on the inside of this "stack" and on through the case. And all four fans are blowing INTO the case. Correct on that? If that is right, then you have in effect a "push / pull" arrangement of fans on the radiator. The RGB fans push air from the outside through the rad, and the NZXT fans pull air through from the back.
3. Separately there were two case fans mounted at the top of the case, and these have been replaced with the new Silentwing fans. The original top fans were plugged into two of the four outputs from the NZXT pump unit, so that is where you plugged in the new Silentwing fans. Now, which way are these fans at the top blowing? Into or out of the case?
- They are blowing out of the top of the case
4. There is a seventh fan at the rear connected to the mobo CHA_FAN6 header. I presume this is blowing OUT of the case?
- It's connected to SYS_FAN6 header and yes blowing out.
I'll have some suggestions for changing where things are plugged in later when I am sure I have this arrangement understood. In the meantime, let me help understand the fan speed readings. If you use the BIOS Setup screens or a mobo utility to monitor fan speeds, it will always label the things it shows you according to what it was DESIGNED to do. For example, although you have the PUMP unit of the Kraken X52 system plugged into the CPU_FAN header, the BIOS only knows that that header is always called "CPU Fan". So it says that, and is wrong, causing confusion. Next, understand that the BIOS and mobo can ONLY show you fan speeds for fans actually plugged into its headers. So ALL of the fans you plug into the output cable from the PUMP unit are completely unknown to the mobo and it can never tell you any of their speeds. BUT the NZXT CAM software utility you have running for that Kraken X52 system CAN read the speeds of the fans connected to that pump cable and WILL show them to you as Rad Fan speeds. It also will show you the correctly-labelled PUMP speed, and that ought to match what the mobo claims is the "CPU Fan" speed. Now, it is quite possible that the CAM software will NOT measure and show you the speeds of all four fans plugged into the pump output cable; it may show you only ONE Rad Fan speed and you are to assume that all the others are the same.
I suggest you check this small detail. You have the front RGB fans and the rear fan plugged into the mobo CHA_FAN5 and ...6 headers. Each of those headers can be used either for fans or for a Pump. When you have such headers, often there is a configuration setting for each of them about whether you are using them for a fan or a pump. The PUMP setting will always run its connected device at full speed. So, check whether there is such a setting and ensure it is set to fan use. Then check the Profile setting for each of these, and ensure it is set to the normal automatic fan speed control, and not something like "turbo" or "quiet".
I'm not sure where to access these settings for each specific fan. I have attached an image of what my BIOS looks like in "Smart Fan 5". The image shows the SYS Fan 6 PUMP settings. However, SYS Fan 5 does not register any fan speed (the two big ones at the front).
Image