Yes, the problem happens with the ADB and AFT, both Eclipse ADT and Android Studio.
The solution I use, in exact step is:
1) hook up the USB cable to the device FIRST.
2) use one hand to align the USB cable to the port but do not insert it. (READY?)
3) keep another hand on the trackpad, moving around randomly.
4) while moving around randomly on the trackpad, insert the USB cable to the port.
5) keep moving around on trackpad for a few second until AFT started.
If unluckily that sometimes I forgot the step and keyboard/trackpad freezes, here is the steps to "recover".
1) unplug the USB cable from Macbook Pro
2) insert a USB memory stick
3) remove the USB stick (optional)
Because the step may involve an unsafe eject of USB, use one of those spare with no data/no important data. I'm sure you will have plenty of this "useless" memory stick around (like 1GB or 2GB, gifts from somewhere).