ML350p Gen8 Noise

[HalcyonOSCS]

My ML350p Gen8 has been making disturbing noise in a strange pattern. Two of the three fans installed are spinning in a pattern like this
6% for a few secs→goes up to more than 20%→goes down to 6%→goes up and repeat.
The other one sticks to 6%.
I am really annoyed by the noise, and I have to put the device in my own bedroom.
Actually I don't mind if all the fans are spinning at a constant 20%, which has a bearable loudness, but the process of fans spinning up makes a disturbing siren-like noise.
I just disabled PCIe 3.0 support for the integrated P420i controller, the pattern continues, but the fans goes up to about 15%, much better.
Here's my system configuration.
1*E5-2670 stepping C1
4*DDR3 ECC Reg 4GB 1333MHz RAM by Kingston
1*500GB Seagate Pipeline (controller Channel A Port 1)
1*2TB Seagate Desktop (controller Channel B Port 1)
No PCI express devices attached
OS is Server 2012 R2
All firmwares are up to date with Intelligent Provisioning the exception, which is version 1.62 instead of 1.62b.
Any ideas on how to completely solve this problem?
BTW the fans spinning up are fan 3 and fan 4, which are at the lower half of the device, where the P420i controller is located. I guess this strange pattern has something to do with P420i, wonder if I can put an LSI HBA on the device and disable P420i.