I'm on a road trip now and I have concluded that the master reset I did recently has corrected the skipping problem. We'll...almost.
Like someone else mentioned earlier I get one skip a couple of minutes after starting my focus and that's it. I thought the master reset did not work because I heard the initial skip. I was starting to think that I didn't hear the follow-up skips and today I am sure after driving more than six hours.
Just to clarify I get skipping from both USBs and SD slot. Thumb drives, iPod, SD card ... They all skip. But now I only get the initial skip and I am cool with that. Hope it stays that way!