The problem so far is BitInstant BTC-e reserves are non-existent. They've not been replenished for a long time now. So until you see some serious "Reserves" amounts listed at
https://btc-e.com/ (reserves are at $33 USD right now), I think BitInstant has to perform "manual" transfers which don't involve the reserves, but some other account that has bitcoins or USD (how much that account has I don't know).
Speaking of which, I just noticed that BTC-e is no longer listed as a deposit method. I don't know if this is old news or how long it's been removed.