Shutdown and possible heat issues

[Borgan]

Hello. I'm new here and have a couple issues i could use help with.

I just recently built a new computer off newegg. It seems to be running fine for the most part except sometimes when I shutdown, windows and the monitor turn off, but the fans and everything else stays on. I don't know if I plugged something in wrong, faulty piece of hardware or some weird win7 function (i'm new to it). I tried just pushing the power button, but sometimes that still leaves fans and stuff on. But if I hold down the power button it will fully shut off.

Also, I've been using HWMonitor and noticed my CPU idles at around 38c, upwards of 48c and the NB idles around 40c upwards of 49c, SB is only a couple lower. I don't know much about temps as I never monitored them before.
The only reason I started now was because i disabled a very loud case fan.
I figure computer specs would be helpful so i'll link them. Hope its not to long.

Antec Three Hundred Illusion Black Steel ATX


G.SKILL Ripjaws Series 8GB (2 x 4GB) 240-Pin DDR3 SDRAM DDR3 1600 (PC3 12800)

EVGA 01G-P3-1561-AR GeForce GTX 560 Ti FPB (Fermi) 1GB 256-bit GDDR5


CORSAIR Builder Series CX600 V2 600W ATX12V v2.3 80 PLUS Certified Active PFC Power Supply

ASUS Crosshair IV Formula AM3 AMD 890FX SATA 6Gb/s USB 3.0

AMD Phenom II X6 1090T Black Edition Thuban 3.2GHz 6 x 512KB L2 Cache 6MB L3 Cache Socket AM3 125W Six-Core Desktop Processor

Western Digital Caviar Black WD5002AALX 500GB 7200 RPM 32MB Cache SATA 6.0Gb/s 3.5" Internal Hard Drive

 

[Novuake]

Do you select 'Shut down' at start menu?

The temperatures are perfectly fine.

 

[Borgan]

Yes I select shutdown at the start menu. Windows turns off and the monitor goes on standby, but the fans and everything stay on.
It happens sometimes when I use the power button on the computer also. Though less often.
When this happens I have to either switch off the power supply or hold down the computers power button to fully shut everything off.