I'm seeing exactly the same thing - I was just about to post up my findings.

I'm on the na11 instance.  I've commented out the subscription and just left the init call in there.  I've also added listeners to the bayeux meta channels, and I can see that the handshake is successful and returns a client id, but as soon as the connect is attempted the server returns a 402::unknown client, with a recommendation to do the handshake again.  The handshake is successful as above, returns a new client id and the cycle continues:

Received message /meta/handshake

Successful = true
Version = 1.0
Client id = er1cv19ubs4rjygn1lw3xvqz489

Received message /meta/connect
Successful = false
Advice =
Reconnect: handshake
Interval: 500
Error = 402::Unknown client

Received message /meta/connect
Successful = false
Advice =
Reconnect: handshake
Interval: 500
Error = 402::Unknown client

Received message /meta/handshake
Successful = true
Version = 1.0
Client id = fc4wk1k9yh6zha1vmn7iyoscgr4

Received message /meta/connect
Successful = false
Advice =
Reconnect: handshake
Interval: 500

I've tried this on chrome, firefox and safari and each time I see the same results.  Reading the bayeux docs, they suggest that the client isn't responding to the connect in time, but I'm not seeing any lags. I've also checked my network connection and that looks okay.  According to one of the posts I've read, dropped connections can be seen if the server is under severe load.  This is happening throughout the day so load doesn't appear to be a major factor.

I'm not sure what I can do to progress this now - its all taking place server side :(

I've just created a java client and that's working okay, so it seems to be something specific to the javascript/visualforce aspect of the mechanism