I was playing online with a friend without problems until we built our first train intersection, where a desync occurred. A few junctions later, we figured out the reason. Should be pretty easy to reproduce, however, in some rare cases and when rotating too much no desync occurred:
>be client on a server
>find a spot where a rail signal can attach to more then one rail:

>select signal, hover over said spot, now rotate until it connects to the non-default rail
>place signal:

[at this point client and host should see the signal connected to two different rails]
>deconstruct signal BAM desync:

>after redownloading the map, the signal is now attached to the same rail as the host saw it:

Greetings,
- Sauerkraut
EDIT: Desync report.