If possible, post a screenshot of your timecode analysis. I don't like mentioning it, but common problems are:
1. People don't realize they need to use timecode, and line-in / thru mode is selected seperately, 2. The sound card inputs are too high a volume (adjust these in the U46 control panel) 3. Either deck is not set to the correct output - ie. both decks output to either 1/2 or 3/4.
3-hour radio show, Mixvibes Cross only! http://soundcloud.com/stealthii/isa3 MacBook Pro 13" Summer-2011 16GB RAM, Vertex-III SSD OSX 10.7.3 Ecler Evo 5 Mixer Technics 1210MK5 x2 Ortofon S-120 OM carts x2