I have a 2006 Concourse ZG 1000, I’ve had it for 2 years.
My question I have is: every time I take it for an oil change it ends up running really bad and twice I was talked into a carb rebuild to get all cylinders to fire.
Anyone have any ideas or experience?

Did they overfill the case with oil? Did they drain from both drain holes?

 Did this just happen recently.  It was running well and now its running bad?   From an oil change??
What does your sight glass show?  Are the same people rebuilding your carbs  the  same people changing the oil?
I would say... Don't take it there anymore. 

Chances are they are overfilling it, then the excess oil gets sprayed out of the crankcase breather into the airbox, where it is clogging up the air filter.
Take the air filter out and clean all the oil out of the airbox, then clean and re-oil the air filter, and it'll run fine.
Oh, and as Mike said, don't take it there any more. 
If you absolutely have to take it there, tell them no more than 3 litres if they change the oil filter, and no more than 2.7 litres without changing the filter.

find a new shop, your current one sucks. .02

Try doing the oil change on your own and see if this happens again!