I gotta go with RobertLynn. I have had pure hell with two 40D bodies and a 70-200 2.8 IS & 300 F4 IS.
All of which ended up replaced with refurbished! The refurbished bodies were great. The lenses are still an issue. I'm worn out. I'm going to rest a bit before pursuing it. Both lenses are USLESS @ wide open.
Stinks that you guys have had issues dealing with the NJ facility. Personally I've only sent two items there (XTi & 300mm f/4L IS), due to a focusing issue and wanted them to take a look at both to help resolve the problem.
I shipped both items together, with a letter explaining the issue. They determined the body was fine, and they even cleaned the sensor for free. The lens (which was out of warranty) was determined to have needed an AF adjustment of some sorts and they charged me a flat $90 fee I think. A day or two later it was all back in my hands and the contents were packaged extremely well in a LOT of bubble wrap.
I've never really thought much on the packaging of lenses, simply because the way I figure they are probably shipping many dozens of lenses every single day and are probably very adept at knowing the limits of their boxes. If history tells them a single layer of bubble wrap and a small box will suffice 99% of the time, and that's the cheapest option, that's what they are going to go with.