Man, you have tried literally everything!
I get the same stutters - but it's not in all software or games. Only the vast majority. And unlike you, my sound doesn't seem to mess up...
That may be a clue. It could be that your OS is waiting for something to happen rather than the game's process.
The thing that immediately pops into my head... in Windows 2000 MIDI files played instantly, and you could loop them no problemo. But in Windows XP opening a MIDI file took much longer, and looping them had delay and audible distortions. Some very smart person finally figured it out:
Do you have any codec packs installed? If not, try installing the K-Lite Codec Pack. It has an option that can take over decoding audio. (even in DirectX games) I have found ffdshow (part of the pack) to be more reliable than the crap Microsoft bundles into Windows - but that's not everyone's experience...
I'd also look through the Sound portion of the control panel. I don't know what you're looking for, but it's another angle to investigate.
And failing that... maybe it is an HDD or controller issue?
Originally Posted by ski-bum
Are you running the Vertex3 off of the Marvell controller? I had the same experience when I tried to use the SATA3 ports with an x58 chipset mobo. When I switched the Vertex3 to the SATA2 Intel controller all the stuttering went away. Not really much differance at all in performance either. Only when you benchmark.
I don't know what it'll turn out to be, but I wish you luck. I myself would like to know the answer.