I merged a lot of posts just now. Remember you can edit your last post for up to an hour.
Windows finding or not finding drivers doesn't solve the issue. However, it's usually older AMD/compatible motherboards with drivers issues, not Intel based. So moving on.
SATA III and 1tb? I didn't realize they even made newer drives that small. Are you sure it's not SATA II?
WD drives do tend to develop bad sectors more often than others. Check it.
Nothing wrong with Windows 8.1, not sure what "of course not" is for. It's a great OS for video work -- just not online work. And since you're using 8, perhaps it's also online? And background tasks are usually the culprit for dropped frames and/or audio sync errors.
Remember to read this: http://www.digitalfaq.com/guides/vid...ped-frames.htm
^ Note: Some of that no longer applies to SATA or multi-core systems, and I'm updating it to reflect that in coming months. Most of it is still applicable.
You can capture to the OS drive without any major issues, but only if a large SATA II/III with dual-core or better specs. Preferable 7200rpm. Intel or AMD. The trick is that it cannot run extraneous stuff, not be on a network, and it not be filled up. The speed and room available on it prevents clashing with the OS. Everything must be at peak operation. But, of course, separate drives are still suggested.
I've seen capturing not liking SSDs.
Onboard audio is usually not suggested, but the Realtek chipsets can sometimes behave and perform nicely. It's the one exception to the 'never use onboard audio' rule. Whatever card you decide to use, it must be tested for distortion, as some have a really awful sound quality.
Audio and video is rarely captured separately. I don't understand where that's coming from. The hardware is often separate, but the capture muxes it immediately.
4 frames over 2+ hours is fine. A bad cut scene or commercial break can cause that. And 2-3 probably happen together. So you probably dropped a few frames twice. But note that your workflow does indeed lose audio sync due to dropped frames. So the video is 2 frames off now. Not noticeable, but you don't want it to skew any more. Some workflows simply drop audio with video, so skew never happens.