I have a GA-EP45-UD3P (rev 1.1)
I'm getting choppy audio only in Windows 7 and Vista on any audio device, including my onboard Realtek, PCI Turtle Beach Riviera and Logitech USB headset. Linux and OS X are fine.
I notice it more when i'm watching video more than I do when i'm listening to music.
I've tried:
Different speakers
Disabling other drivers on other devices one by one and playing video
Uninstalling and reinstalling fresh drivers from the GIGABYTE website and motherboard CD via 'update driver' rather than self installing '.exe's for each audio device
Unplugging all non essential devices including ethernet lines
Going in the BIOS and turning off Azalia and trying other audio devices and speakers
Running MSCONFIG and booting with only essential startup applications and services
Testing my memory (reported no errors)
Using all versions of the 'rev 1.1' BIOS to date
Finally I ran a latency check:
http://www.imagebam.com/image/290dd343992556/A couple other people I know with the same motherboard have the same issue on Windows