MOST important is: are you converting to AVC or HEVC?
The HEVC software encoder in ffmpeg is limited to a max. number of threads.
Then: the "Bars" in CloneBD: I understand, that the first 3 are maxed and the last one is not (screenshot would help a lot in getting picture of things)?
That would mean, the encoder is limiting.
Then there is another thing: do you have Cinavia removal enabled? (Downconvert audio and AnyDVD removes Cinavia).
For technical reasons, Cinavia removal needs to be serialized, so it can't use multiple cores. With many audio streams, this can be a limiting factor, too.
Regarding GTX980 being slower than your limited CPU: I find that very hard to believe. Can you give us numbers? (fps on an average AVC source Blu-ray with and without nVidia acceleration).
I have a 950 and frame rate usually is >300fps (if not limited by the source or destination medium - so using SSD for both).