Sucks that no one replied to you. I am running into the same issue with my DDJ-1000. I HATE that. I don't know why it sounds wobbly/warbly.
DVS is FINE. Perfect.
There's nothing wrong with the DDJ, as I tested it out with Mixxx and Traktor and the jogwheels scratch perfectly. Rekordbox thing? I don't know.
I had a low-end DDJ controller too, and my scratches were a lot tighter... there's some weird digital artifact with the DDJ-1000 AND the DDJ-800. I tested them both. We're not alone.
Pioneer.. what is up? Rekordbox thing? I tested it out with version 5 AND 6... same problem. People have said this issue is not present with the DDJ-400. I haven't tried that.
Tried DDJ-SX with Rekordbox, and the scratches do not wobble / warble. It's more obvious with slower/medium speed stuff ESPECIALLY on vocal samples. It's painful-sounding. Sounds terrible on hip-hop cuts.
I'd REALLY like to know what's going on. I don't want to return my 1000 and get some random mixer just to scratch with DVS. I'd rather have all the cool options that the DDJ-1000 has, in addition to that nice fader.
Any luck with your stuff?