The physics also messes up occasionally. Was playing today and noticed that the breast bone(s) closest to the chest were working fine but the outer most/forward most bone (ie. nipple) was pointed nearly straight down. Once it does this, I am not sure if there is a fix or if it ever goes away. Equipping various tops doesn't fix it. Disabling the Physics out of Combat option puts them to rights though it turns off the bouncing walk.
Not sure what I did to cause it. I did encounter the nav mesh and repeated jump issue you mentioned while stuck in the bottom of an elevator shaft. Cannot say that it is related since I didn't immediately check myself out afterwards.
Should also note that I only noticed it on the MC, not any of the NPC so probably something I did.