The patch didn't fix the broken Companion quest for me so I've just gone back to my Lvl 38 save, bit miffed as I was Lvl 52 with lots of nice things
Ah well, at least I can change my character a bit this time & I know what not to spec in!
If this is where you've finished Bloods Honor (killing the Glenmoril Witches) resulting in the next quest failing activate when speaking to Vikas and members of the Companions standing outside Jorrvaskr, then there is a work around.
The next quest that should activate is called
Purity of Revenge
Advice on the Internet at The Unofficial Elder Scrolls site stated that you had to wait one in game month for the Dungeon at Driftshade Refuge to respawn. It appears that a lot of problems with this quest revolve around people entering Driftshade Refuge to complete another quest.
There was a rather ominous warning that "There is a chance that waiting the 30 in game days after clearing Driftshade Refuge will NOT correct the glitch. Also, entering Driftshade Refuge before the quest activates may not fix the problem either. If Driftshade Refuge has been cleared prior to completing Blood's Honor, no matter what, there is a chance the quest is forever lost."
So since a month in game had elapsed, I backed up my saved games and I did what the bugfix suggested.
First I opened up the Console, then with Vilkas in front of me in Jovaskrr, I typed the following
setstage C05 0
This removed my existing companion and added Vilkas (as it should do doing the quest normally) - I then got the updates for Purity of Blood in my Journal and off we went to Driftshade Refuge.
Completing the quest and then returning to Whiterun sucessfully updated the Journal and advanced to the next Quest. I can confirm that all NPCS returned to their normal behaviour and everything seems find again.