My V3 sub-03 does the same thing. I sent it back to Cobb under warranty, but they said nothing was wrong. They think something is wrong with my car, but my standard OBDII Bluetooth scanner works perfectly fine.
2008 Legacy 2.5GT spec.B, stage 2, Snail Tuned, ERZ Catted DP, SPT Cat-Back, Epic Springs, Hotchkis Sway Bars
1990 Miata, FM 1.8L Swap
2001 Miata, FM V-Maxx Classics, 15x8 Jongbloed wheels