I haven't had any issues with coinbase xfers.  This is not cash from a banking secrecy standpoint as it is an electronic transfer.  BSA is looking specifically for 'cash' at the bank teller level when talking about the nice little form they give me attitude on

The real quesiton is what kind of reporting requirements does Coinbase have.  I'm not sure they have any right now, but I'm betting it will become like a 1099-k (Paypal) or 1099-B (brokerage) in the future so that the IRS knows what's going on.

Since the IRS has declared btc to be property, be sure to hold large amounts 1yr +1 day so you can get capital gains treatment.