They were the old boxes they had lying about . Apparently the charge was for storage and handling !
In that case it could perhaps be considered a bit cheeky. In the defence of bike shops though I would say that I empathasise somewhat with their situation on things like this. People buy stuff cheaper than they can afford to sell at CRC/Merlin etc and then still expect to go into the local bike shop and get things like boxes and other help free of charge. Not saying this is what your friend does/has done but having been on the other side of the argument I can see why bike shops are sometimes reluctant to do things like this.
Bit of a catch-22 situation though as if you don't provide friendly service then people might not come back, but at the same time they might just still buy at the cheapest places regardless of effort/service provided by the LBS. If he is known to, or a regular in said shop there is no excuse though!