Indeed, James, we've been facing that problem all along and have learned to live with it. The best solution I can suggest is to have shipyards all over the place so that if this happens your ship isn't pushed too far off their scheduled route.
I tried a few more times to connect last night and couldn't stay connected for more than a few seconds (sometimes an instant desynch). I managed to place two stations after about 10-15 connection attempts. I think I also built a ship but wasn't able to get so far as put holds on it.
The clock is really jittery, shooting ahead, stopping, shooting ahead again. I assume that is occurring on the server side as well which is causing the desynchs. We'd need a mechanism to keep the clocks more in synch so that this doesn't happen.
EDIT: I think what's happening is that when you perform a function in the game and your client is waiting for confirmation of the action from the server and it enters one of its frequent multi-second pauses, the client signals a desynch because it hasn't received anything from the server. At least, that's how it feels. When I am lucky enough to not desynch immediately on connection, as soon as I perform any action it will likely desynch because it will hit one of the pauses and time out.