Problem is exact following: When the nether is getting unloaded its causing massive lag (not FPS, but lag like latency, block-lag, or whatever you want to call it).
I am literally going mod by mod now, to see which one is causing that. Fortunately we know when it started to happen, so I can just look at the mods that were changed in transition from 2.1.5(6) to 2.1.7. its a fair amount of mods and the slow pack loading is not really helping
edit: also after you leave nether, and you wait for few minutes, it will fix itself. but again when nether will get loaded, and then will try to unload... bad stuff happns again.