I always loose the communication between TS 2.0.5 and my ms3 with rc1. I was on beta 18 and beta 20 before and I was having the same problem. I also tried with TS 2.0.0. Nothing changed.
I tried with the usb port of the ms3 and also with the serial to usb cable that diyautotune sells. Same problem.
At idle it seems ok but when I hit the gaz pedal, I almost always loose the communication. But sometimes I can make a pull before loosing comm but it's rare.
I tought it was noise so I added 220uf to the 12v input f the MS but nothing changed. I already have a capacitor on the ignition (near the 6 pen coils). I also added 104 caps on the 5v of the 40 pins socket.
I'm using 6x 2uz pen coils and 6 low impedance injectors with resistor box.
In datalogs, battery voltage is stable (I also have a capacitor on the bootloader jumper).
All my grounds are good, directly on the intake and the sensors ground is only connected to the MS.