1) The fan speeds could possibly be too low to measure accurately. All analog fans I've ever used do this (using my first PWM fans now, doubt their measuring method is any different though, but you DO know the power cycles used), usually when approaching 600 RPM the readings either drop to zero, freeze or become erratic (the most common scenario).
2) Normal. The power that's not going to the fans has to be dumped somewhere, and that somewhere is the controller, which releases the energy as heat - and it is on the receiving end of the full power load without any mechanism that requires it. 80'C and 105'C are common temperature ratings (maximum operating I think) for capacitors, for example, so if something feels "warm" or even "hot" to a human, it's still probably well within accepted operating parameters. The old BigNG controller I have even employs a heatsink, and for a good reason too!
Case: Define Mini
Parts: P8Z77-M Pro µATX, i5-3570K, N650Ti-1GD5/OC, 8 GB G.Skill DDR3U, Xonar DX, WD G 1 TB, mx100 256 GB SSD, RX-5300 PSU
Cooling: Noctua NH-U12P SE2 + Scythe SS PWM, 2x Noctua NF-P12
Extras: Eaton UPS, Dell 24" EIPS, Ducky TKL, SteelSeries Sensei Raw, Synology DS213j 6 TB NAS
idle-load: CPU 32-44 °C @ 300/600-600/800 RPM, GPU 35-65 °C @ 1200-1650 RPM