Here is my setup. 2 ESC's(1 bec disabled), 2 Li-po's, 1 Y-connector. Motors both run, but while advancing throttle the Left (bec disabled)accelerates normally, then the right(bec enabled) accelerates but always behind the left. While reducing throttle, right stops before the left. What am I missing here?

You poor thing ... lucky that there is the net. I was helping a friend with this problem and it took me a few days to figure it out. Hehehehee ... Its simple. If the difference is very little, a click or two then there is no real issue but if its more than just a couple of clicks then you will have issues. Your problem may be that the motors will not be giving the same amount of thrust. You can check this with 2 watt meters. This is usually caused by cheap ESCs. We had that problem with the cheap ones and when we changed to branded ones it was resolved.

Sometimes you need to go into the esc programming and adjust throttle parameters to get them to accelerate and decelerate evenly (and also LVC). However the biggest problem is jsut what was stated above -cheap escs.
Walt

Castle Creation's Scribe publication has a good guide to setting up dual brushless power systems. Check out pages 2 & 3 of the link below:

[link=http://www.castlecreations.com/media/castle_scribe_archives/Castle%20Scribe%20CE-03-Mar2006.pdf]Castle Scribe March 2006[/link]

Below is a graphic from that article summarizing what they recommend:

Aaaaah ... a single battery pack is best ... got that!

Thanks for all the info.

Al