If you could play them in itunes, would indicate that Itunes knows where they are, not necessarily that they haven't been moved =P. Just to confirm that isn't the issue, could you go into traktor, And on the left hand side, expand the itunes library. From there, try play a song that wouldn't play before (Rather than trying to play it straight out of your traktor library). Will it work?
Half marked sync just means that it isn't the Master deck. As rule of thumb, whatever deck you play first is master (If you have sync turned on the other decks, you will find their tempo faders are greyed out, and you can only adjust the Master deck. Master = The box is orange, but the writing is black. A slave deck is a grey box with Orange writing... Although the colouring might be slightly different if you are using Pre-traktor 2.0, it still functions the same way).
Regardless, as I mentioned earlier before. Sync by default doesn't match the phrasing of the tracks, just the tempo. You will still need to push them into phase with each other. If you want it to stay in phrase, enable quantise at the top of the screen. Otherwise turn on Beatsync in the options (See the earlier link I gave).
Your other problem could possibly be bad beat-gridding. See below links for more information
http://www.djtechtools.com/2012/04/2...s-eans-method/
http://www.djtechtools.com/2011/10/2...-in-traktor-2/
Cue points still work with Timecode Vinyl. You just press whatever hotcue you set and it jumps. I don't understand what you mean by 'start automatically' though. Could you please elaborate?
Honestly, with traktor pro 2 being so cheap... if you're using an earlier version, an upgrade might just fix all your problems.
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