It would be interesting to know a little more about the process for creating the public / private keys.
It could be that the thief is an insider, or that someone has figured out how to attack a number generator for a particular connected chain.
As most respectable coin makers wil tell you, you should never retain any copies of the private keys, and they should be destroyed after they are applied, so something like this would not be possible.
Plus the computer you are generating these keys with should NEVER touch the internet.
So a "connected" chain is a very bad idea.
thanks!