Using both my line 6 GX and my Fast Track Ultra, I have seen the result of a 'bounce to tracks' mixdown include skipping.
 
In every case restarting the computer has caused the recurring problem to stop recurring. That said, when it has happened once, it isn't guaranteed that it will happen again the next time I bounce.
 
I use a windows 8 x64 computer (2 core) with X2 x64. I'm not sure I can make it happen.
 
In one case, I exported the bounced track to a wav and burned it to a CD before listening to it. I first experienced it using RMix, and thought the problem might be related to that, but tonight, I experienced it on a project with no RMixes in the project.
 
If it happens again, I'll post an mp3. So far, I've just deleted the mess-ups and re-bounced. I've never heard the problem while just playing the mix. I have to bounce to tracks then solo that bounced track to hear it and the skips are materialized in that track. When I export the track, the skips are exported too. One time, I heard the skips and ctrl+z back to when I got a track with the skips and it was the bounce to tracks when the skipping was introduced. 
 
I hesitate to post this, but I'm pretty sure after tonight, it's worth sharing. I have no repeatability information yet, but I'm hunting for it.

http://stabilitynetwork.blob.core.windows.net/sn-blob/skippy.mp3

Ok... here's an example. The skippiness was added when I tried to normalize the mix. I was playing the mix at the same time I tried to normalize (Alt>P>N). The result was this skippy track. It's not always how I end up with a skippy track, but it was in this case. Does it have to do with processor load? Not sure.

It could be your audio drivers.  Try turning off the 64 bit audio engine and see what happens. 

Also just to be sure you don't have different sample rates in that projects do you? One thing I don't understand is you mention different audio devices could they be out of sync?

What are your system specs? 

You have some good talent in that song. 

Thanks for the nice words, John. I don't use the different interfaces at the same time. I use the Line 6 when I'm moving around mixing. I carry it in my AlphaTrack bag case in the little pocket. I mentioned both to say that I had tried to rule out drivers by seeing the problem on 2 different devices. I haven't tried turning off 64 bit audio engine.

I was kinda thinking it might have more to do with background threads in Windows 8. I know that there is some tricky work for the new app model (metro or whatever) where when the apps fall to a back ground thread their behavior changes. I am wondering if this is in play.

Whenever I look at it, it works fine. It's only when I'm multi-tasking that I get the goofy behavior.

I heard once of a guy who wrote a keyboard driver for his boss that only threw in random keys that were near the keys typed when his typing speed went faster than a given keys per minute. I thought this was hysterical. When he slowed down, the problem went away, but when he typed quickly it would screw up. Ha ha. What a great April Fools.

This problem seems kinda like that. Whenever I watch it, no problem. When I get busy and am not paying attention... bang.

I think the best most repeatable test is to Normalize a track during playback... Select a clip, start playback, normalize... any issues?

I'll try repeating using this and with x64 processing on and off.

I have only 24 bit 88.2 audio in the project.

http://stabilitynetwork.blob.core.windows.net/sn-blob/base8.htm
Here are non messed up versions of the songs. BTW, if you hear things in my mixes you would do differently, feel free to tell me. I'm always open to suggestions.

I went ahead and created a problem ticket on this one. I can pretty reliably reproduce it. No one else, huh? Any Win 8 people out there give it a test?

I don't think many people have got on the Win 8 train yet.

That's the strangest symptom I've ever heard. It's as if the disk file itself is corrupted. Do you have another hard drive that you can try exporting to? Or even a flash drive?

Thanks for the responses. It's definitely not the Hard Drive. Everything is fine except this occasional annomaly. As long as the skipping is obvious and severe as in the example I posted above, it's easy to restart and rebounce leaving the focus on Sonar while I bounce to be safe.

Interestingly, I find myself listening very critically to mixes wondering if a note picked early might actually be a skip. They have never proved to be when I looked closer. It was always an out of time note played by the performer.

What I'm saying is that when I get the skipping it is obvious and severe, otherwise non-existent. It's not like I'm getting grades of the problem that get so subtle I might miss it on listening. It's either skipping or it's not.

The first time I saw it was on a straight bounce to tracks where I was bouncing 14 or so audio tracks and some busses down to a stereo track.

Subsequently, I have not had a lot of repeats at this stage, but I have seen (and repeated it) by playing a track and while the track is playing, normalizing the same clip I'm playing (the clip is probably solo'd at the time too). The clip would be routed direct to the audio outs... not to a bus. Flipping the 64 bit processing switch didn't help.

Not sure what it is yet. I posted a problem ticket with Sonar, but I'm not sure how easily they will be able to repeat it.
 
As a re-cap, I have experienced it identically using two different audio interfaces Line 6 GX (small one channel thing for travelling) and m-audio fast track ultra. In both cases, Asio driver mode. (I was not using both interfaces at the same time).

BitFlipper >
Just re-read your post, and actually I do have several hard drives... ok.. 4. 2 Drives are internal to the PC and 2 are in an IcyDock. I have experienced on the D: (non-system) drive on the laptop and on one of the two IcyDock drives too. So, I am answering that I have seen the issue on more than one drive.

Bit>

More on the drives, just in case I have Enable Write Caching and Turn off Windows write cache buffer flushing checked on the internal drive. Perhaps related? I'll try replicating the problem with different settings.