This could be a problem with mixed chip generations indeed. Have you monitored with GPU-Z or HWMonitor or the likes though whether the Folding jobs were really executed on the 1080Ti still?I put my gtx660 in to see what would happen, if the board would let me use it as a primary driver and well i was in for a rude awakening. My 1080ti suddenly then couldn't even do 11k ppd estimated. I remove the 660 and the 1080ti is back to norm on its current unit and a 1.1mill estimated ppd . I heard this could be a issue mixing gpus but prob not gonna bother getting a gpu for this thing then. It could be a generational thing but i did fresh reinstalls of stuff and it made zero difference.
In the past, I had dual GPU mixtures of AMD 7000 series with Nvidia Pascal, as well as combinations of slightly differently sized Pascals (1070, 1080, 1080Ti). This never made any problems for me, besides the little inconvenience of having two GPUs of different throughput in the computer. E.g., it puts some more mental arithmetic into buffering BOINC GPU jobs and performance monitoring than if there were only same GPU models in the computer.