It's possible that it's point to point and repeated rather than being a true, fully shared bus. In that case you may only be seeing a fraction of the communication. Sounds like the connection to the junction box must be special in some way in any case. Maybe it handles termination of some kind.
I would guess that they repeat the signal to tolerate errors introduced by voltage swings when the servos start. The di2 pos signal seems to repeat for over a second. Although it is clocked much slower.
http://people.freebsd.org/~jeff/bikes/shift1.jpg
I have a really crappy USB scope at home but if it's a 1mhz signal it should be easy to make a high pass filter and see if I can interpret it. If I want to do anything meaningful at that frequency without hogging battery I need to be able to use the bus from a micro clocked no faster than that so I can't bitbang it in software. If it's too far from actual CANbus spec it might require a custom IC.
Thanks for the update. I should have a kit in a couple of weeks to look at. I'll cut some wires and stick the probes in circuit and report back.

). That wasn't really helpful since the top of the micro-controller is blacked-out, all parts are so freak-in small, the PCB is at least 4 layers, etc. But there is a direct connection (both for ground and power/communication) between the shifters and the wire going to the battery and derailleurs.
Unfortunately that would have to wait until I next flew stateside.