I guess it's all about qualitative interpretation of 'quiet'.
Though my system is an i140 instead of an i160, for me it is very quiet at idle, but definitely not what I would call silent.
I think you're probably hearing the pumps, which produce a very slight hum I can barely hear about 2 feet away, but which are noticeably louder as I get my ear closer.
Unless you top exhaust fan has an issue, you should not be able to hear anything unless it's 400+ rpm.
Maybe the HDD-like noise you mention is really the SATA HDD. Even without activity, it will make noise as it parks its head. It's definitely a loud sound compared to the rest of the system.
Also the GPU board has a small fan over a heatsink which can rattle/shudder somewhat at high speed, as observed on some systems. Not sure if it's your issue, but it's easily identifiable as the noise is very localized to the GPU radiator side.
Otherwise your temps and pump speeds look absolutely nominal. Pumps are supposed to be fixed speed ~1850-1900 rpm.
The +100C motherboard temp #1-#3 are of no concern, they're not valid sensors. Only #2 is correct one, as shown in MSI command center and/or BIOS
For the software, I suppose you mean Corsair iCue rather than Corsair Link. The iXXX Corsair One systems are only supported by iCue.