Other people have reported similar problems, but then I can not really think of anything we modded that might have caused it. Generally the game seems to have become a bit more wonky with the last warband patch, with animations skipping frames and the like.
Unless the fault was with your connection or low fps because of the strange single core usage by warband I could really not see any way that the problems you describe should be worse in Vikingr than in native or other mods, so there is little we can do about it.
We neither did great changes to the hit detection (yet), nor did we do anything special with throwing weapons that I can think of. The only explanation I could think of is that combat in Vikingr is so much slower and concentrated that a single odd strike is much more easily noticed than it would be in more fast-paced warband mods and native.