OK...I'm fairly certain this issue is directly related to the "follower-won't-leave-you" bug, usually in conjunction with Companion quests. I had an issue awhile back where Farkas kept running after me, even if I told him to "part ways". He eventually ticked me off enough that I killed him - big mistake. I think the game still thinks Farkas is following me, though he's lying face-down/ass-up in a meadow somewhere. This is unfixable, and several other forums indicate that unless you go back to a save point before the "event" you can't undo it by waiting, taking on other follower quests, or by any other means. I guess I'll have to shelf Skyrim in favor of other means of entertainment until a patch comes out for this issue, since it's now brought the Dawnguard quest to complete halt. Thanks Bethesda...great programming.
I had this exact thing happen to me. I entered Whiterun, I see Farkas charging at me down the street running all the way from Jorvaskar. He gets to me and opens a dialog screen. I dismiss him, he does it again. Following me and harassing me. I try to leave the city, he follows. I tell him it's time to part ways, he agrees but ignores me.
What I did was I unequipped my weapon and punched a guard (four times to initiate combat). All the guards turned on Farkas, killing him. Oddly, they left me alone. That fixed the problem. Later that evening, a courier tracked me down at my home in Markarth informing me of Farkas's death. It seems the big dope had me in his will, I kept the note and the meager sum of gold.
Sad story, but that's not the end of it. It gets weirder from here!
Whiterun is my center of operations. I am there often and over the next few days of gameplay I had to pass over poor Farkas's corpse, dead as a doornail. It made me sad seeing him, I really did like the big stupid oaf, so I decided to drag him out of the gutter like some sort of huge nord roadkill and placed him on the lawn of the Temple of Arkay. A proper Nord burial for my poor, over-eager friend Farkas.
Days pass. I was in the process of leveling so I could encounter "A Legendary Dragon". On today's menu was leveling heavy armor. I arrived at the courtyard behind Jorvaskaar with my zombie thrall, a dunmer bandit chief now paying the price for his life of crime. Had he known that this is what the afterlife held in store for him, he may have decided not to set up that skooma den north of Riften.
We started to spar, me defending and healing, my pet attacking. Hard work, but I could feel my proficiency with heavy armor increasing. The companions always enjoy watching me spar with my unfortunate thralls and soon they had all gathered around to cheer and place bets. Popular money's always on "the big one". Me invariably being "the small one", I can't help but be a little offended. I peer out from behind my dragon bone shield at the familiar faces. Fierce Aela, noble Vilkas, Athis, the best sword-arm with a short blade The Companions had to offer. Even timid Ria was cheering from the shade of the back porch...and..who is that with her? None other than
FARKAS! BACK FROM THE DEAD!
I couldn't believe it. I lowered by shield, signifying to my zombie slave that our sparring session had ended. I ran up to Farkas and welcomed him back by paying for some heavy armor training!
It was a miracle of Arkay, I tell you. I think Vilkas had tears in his eyes, the milkdrinker.
