Let us analyze, by removing the fluff.
Although a cause for concern in farmers, inflammation in female dairy cattle, which occurs commonly after they give birth --
many disorders, including metabolic diseases such as ketosis and fatty liver, are known to occur at this time -- it is believed to play a beneficial role in the complex process of going from late pregnancy to lactation.
(A) Although a cause for concern among farmers, inflammation in pregnant female dairy cattle, which occurs commonly just after birth - it is believed to play a beneficial role in the complex process of going from late pregnancy to lactation
WRONG - double subject error, as first independent clause is not complete.(B) Although inflammation in pregnant female dairy cattle, which occurs commonly just after birth, is a cause for concern among farmers
CORRECT - also "which" non vital modifier correctly modies inflammation, in pregnant female dairy cattle - prepositional phrase is vital modifier for inflammation. This is exception to touch rule in which a vital modifier can inserted between noun and non-vital modifier.(C) Although a cause for concern among farmers, inflammation in female dairy cattle, occurring commonly after birth
WRONG - same as A, double subject error.(D) Occurring commonly after birth, inflammation in female dairy cattle is a cause for concern among farmers
Looks wordy to me, also there is no expression of although to give a connection in terms of meaning between two clauses(E) Inflammation in pregnant female dairy cattle, which occurs commonly after birth, although it is a cause for concern among farmers
WRONG - same as A - double subject errorExperts, please add/correct if anything wrong.
Thanks