I'm fairly confident this is a program hogging resources that don't seem to show up on the Task Manager. I use FFmpeg Batch AV Converter almost constantly and it seems to be Multi-File encoding that is the culprit. My video card supports 5 encoding streams but strangely using more doesn't make things go faster....it just seems to bring the system to it's knees.
The FPS of the encoding is almost identical whether I do one encoding at a time or 4 which means it is not faster to do more than one but it seems to affect the rest of the system in an adverse way. I use paint.net a lot to touch up movie posters and when I run more than 2 encoding streams at once it is constantly not responding, but when I run only 1 I have no issues as of yet but the overall encoding speed isn't any different. Go figure.