My main test and development Portsdown 4 recently started suffering from this problem. I think that the problem was too high a voltage (5.2v) being supplied to the Pluto through the USB cable. I reduced the Raspberry Pi supply voltage down to 5.05v and the problem has gone away.
The LimeSDR has always liked a healthy 5.2v USB supply voltage, so I have been encouraging everyone to set their Raspberry Pi 5v supplies to this level. Whilst the advice remains valid for the LimeSDR, my advice for the Pluto is now to set the Raspberry Pi supply to 5.05v at the GPIO connector.
Please let me know if this cures the problem for you.