This may not be that helpful in solving your problem, but I have my AR slaved to Logic X and it works fine with the AR in song mode – always starts in the correct place. (Looping in Logic is another matter, but . . . ).

As for starting mid song, I usually put dummy MIDI objects on the AR track which are the same length as the patterns, then you can always make sure you’re starting at the beginning of an AR pattern.

Good luck with it, anyway.