Repair to new equipment

I have a question about some repairs I had done at Canon, Irvine. I was having focus problems with my new 5D2 and new lenses. I could not get the auto-focus to work properly. I took my camera body and all lenses to Irvine. I explained the issue and the girl said to leave my body and all lenses with them. In addition to the body I dropped off my 28-300L, 100-400L, 24-105L and 17-40L, All new(less than a yr old). All were covered under warranty. I received all of my equipment yesterday and looked at what had been done to each piece of equipment. They replaced the focusing screen in the body and found hot pixels which they say have been repaired. They said the camera was front focusing and that has been corrected with electrical adjustments. Also, ALL of my lenses required adjustments. My question to the forum is, Is that normal? I just spent quite a bit of $ on this equipment. I would think it should work out of the box... Are my expectations too high? I have not had the chance to try out any of the equipment yet but will this afternoon. Hopefully all is correct and it will now take sharp photos.

I had a similar experience with a brand new 50mm f/1.2 lens. It was back-focusing by almost a full inch, straight out of the box. When I called Canon, I was told I'd have to pay for shipping to have it calibrated, and would need to give up my camera body for a couple of weeks, too. Didn't I just pay $1600 for a piece of equipment that by all rights should actually work? Fortunately, I purchased from B&H, who exchanged it and paid for the shipping to do so. Frankly, I didn't think they should be the ones to eat that cost.

The new lens back-focuses a bit, too, but not nearly as much. I've got a 7D coming in later this week, so will be able to micro-adjust now.