It is hard, or maybe not even possible at all to make the auto config work good on every system with different cpu combinations.
Ver 0.1.7 does the threads & affinity calculation in auto mode based on available L3 cache sizes, where 0.1.6 was not . The logic used there was really poor

So you can set
--cpu-threads 15 by hand, without affinity set at all with the HT off, and should get the 4900h/s again.
Yes, I could probably use --cpu-threads 15 without Hyper-Threading enabled to get the 4900h/s again, but this is not that I would like to know.
I would like to know how can we use the Hyper-Threading to get a better hashrate.
If we can get 4400h/s with H-T (Hyper-Threading) enabled and only 55% processor activity with 16 thread out of 32 we could probably get like 30 or 31 threads out of 32 and get like, 7000h/s (x1.6)
EDIT : with --cpu-threads 15 without H-T I have 4900h/s again
Nico