Marketing (for example, BFL equipment is much prettier than Avalon).

What kind of proprietary knowledge do they have, that there are these long waiting lines for the machine?

None. But they do have capital, which they got by having a fairly good reputation from making cheap FPGA miners which they could do because they found a way to buy obsolete Altera FPGAs really cheap.

What is they key issue that makes these boxes so hard to replicate?

People who know what they're doing don't design Bitcoin mining equipment. There are probably a lot of different reasons why, mostly due to very high financial risk. The only people designing this stuff are incompetent noobs, with predictable results.