Have you tried reinstalling the drivers? Have you tried using speakers?
I have an Asus laptop which has some weird power saving function and some audio software. If it's in battery saving mode, the jacks don't work. Maybe your mobo has some similar features/problems?
Motherboard: Gigabyte ma-770t-ud3
CPU: AMD Phenom II X4 955 @ 3,7Ghz
Cooler: Noctua NH-D14
Memory: Kingston 8Gb (2gb x 4)
GPU: Asus Gtx 480
Case: NZXT Phantom
PSU: CoolerMaster Silent Pro M850
Monitor: LG W2363D