For example, I edit a line, changing minimum load or waiting time. I close the window. An hour later the change still hasn't registered. It's as if the orders never reached the server.
If you edit the minimum load or waiting time for a convoy that is already at a stop, the change will not take effect until the next time a convoy reaches that stop. I
Sometimes you can open the Schedule window of the waiting convoy, manually send it to another stop, then do the same again to send it back to the same stop so the changes work. But it's a hack and normally you won't even be able to open the Schedule window.
It's also possible that you are lagging behind the server. There might be things to improve this, but we would need to know some things about your setup (Linux or Windows, how much RAM, what CPU).
2) Looking at the Congestion numbers in the Town Hall, it seems this has happened only recently (a few months). When I started the line, traffic was OK. Why?
It's probably the effect of your buses and traffic lights.
The most important source of Much Hudton's traffic jams is that the village is divided by a railway line, which is only crossed by a long level crossing (maybe the longest in the whole map!) and a weak (wooden trestle) bridge. I know you don't have much money, but you might want to try to improve the bridge situation or change the bus routes so this does not affect them so much.