I go with the theory that it's a combination of Havok Behavior and Havok Physics, someone posted that earlier in this thread. It seems fairly obvious to me that Actors do have certain Behavior features that the player character lacks.
Since the issue is being defined by Gstaff as a being 'havok related' and the problem only affects NPC's...
With the issues of adding completely new custom animations (not simply replacers)... Could the problem perhaps be in the hkx files somewhere themselves that 'interact incorrectly' with the ground collision?
Just a random thought as I was reading through this thread after just reading the havoc convertor thread.
Unless I'm misunderstanding (most likely

) was this where you referring to my post (above)? If so, here's the http://www.gamesas.com/topic/1336657-rel-havok-animation-converter-thread-2/ on it...
On the plus side, TheHologram thinks he has a breakthrough... So perhaps his breakthrough might be/lead to a resolution to this problem.
As another thought... if the problem can be identified (either exactly or as 'close to exactly' as possible to lead programmers to), perhaps it might be something the SKSE team could do something about? I have no idea as I'm most definitely NOT a havoc type person... I just slept at a holiday in express last night!

(no not really - I just devour the forums all over the place

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Non-useful Rant - read or not (probably not

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Spoiler
As to Beth refusing fix this problem and shove it off as being a havoc issue... It wouldn't pass the filters here what my thoughts are on it. I will say this however; Beth, you aren't getting any money from me in any capacity again unless you get your >self censored< together and learn to properly QA your stuff... The purchaser of your product should NOT have to rely on 'unofficial patches' that fix 100's (or thousands) of bugs in the game, some as directly obvious as quests... and while you don't have to release any type of mod tool to the community, the fact that you do we appreciate, but I believe it is a flat out impossible that you all used the CK to make skyrim... look at the bug list for the CK and then try telling that to us again.
Sorry to harsh on Beth in this thread, I'm more than a little ticked, but I'm not sorry to harsh on Beth... Tossing the vast majority your problems onto the mod community is rubbish. At least have the courtesy to say thank you to the modders who fix your broken software currently and in the past. Why? Because without them you wouldn't have had the longevity of previous titles as you have. Show some class rather than corporate greed... you did just make 600+ million dollars,the least you could do is say 'Thanks, nice job!" or somesuch... and no, this is not directed at the actual developers who have been all over these threads trying to help us... it's at the 'suits' at the top that this is directed at.