I had the same kind of issue with Arduino Uno only powered by USB ; I mesured the voltages on the board and hadn't more than 2.9V which is to low to power steadily the RN52. USB voltage from my PC motherboard was too low : around 4,75V instead of 5V.
U6 chip needs a minimum voltage to provide a good 3.3V to the whole board (5V mini if I remember well).
The best would to power the arduino board with an additionnal DC power supply (recommended 7 to 12V), it should be ok then.
I suggest to follow this
web page to connect the Aduino Uno to the BlueSAAB ISP. Upload ArduinoISP sketch to Arduino Uno board, then burn bootloader and upload SAAB-CDC code using "Arduino as ISP" under Tools>Programmer menu.
Good luck, that's an amazing device !
01' 9.3 SE Conv - AS3 - Nexus 5 Android M 6.0.1 - BlueSaab v4.2 + Amp - Latest CDC repo.