According to znort's blockparser code, 1Q6nyjSQ79AAw67xAGHgXxXHRj9erLLqhD is now provably in the same wallet as 24550 other addresses. I used that list to find whether there was any connection between these addresses and the large 1Dky... address. There have been 86701 inputs and outputs to/from these 24k addresses, all since 18th June. It seems the Silk Road wallet must have been reset relatively recently, or we'd see older transactions in the list.
Here's your 0.001 BTC being grouped with a few other silkroad addresses:
https://blockchain.info/tx-index/13896290
Notice that 1AVMrqGmoJ7Jpjh7FdbHnDwK34VBxtBCcC is an input to the same transaction. That means that both your deposit address and 1AVMrqGmoJ7Jpjh7FdbHnDwK34VBxtBCcC are in the same wallet - silk road's wallet.
Then look at this transaction:
http://blockchain.info/tx-index/11928355
It's a big payment to the mystery large address. 1AVMrqGmoJ7Jpjh7FdbHnDwK34VBxtBCcC is one of the contributors.
The most recent two deposits into 1Dky... were also from addresses on the list of 24k silk road addresses obtained using znort's code.
I think that's pretty conclusive proof that the large address is related to Silk Road.