Hi, this has nothing to do with yor CPU, i'm having the same problem. The PlutoSDR uses libiio, which is a piece of software by Analog Devices handling all the USB stuff. but the problem is, that i need to poll the data, which means, that i need to ask it for a new chunk of samples. If i don't manage to do it frequently enough, there are lost samples. And that's the worst thing that can happen for a DVB-S demodulator...
There are many reasons for this problem. It can be the operating system not scheduling the thread often enough which does the polling. That's the case on high CPU load, or if there are peaks in CPU usage. Of course, this is an important problem, which i need to find a solution for. A temporary solution could be using lower samplerates. That improves things a little, but it doesn't fix the problem. I recommend other SDRs at the moment until i come up with a solution. As far as i know, the PlutoSDR and LimeSDR have this problem. I'll keep you posted on this.