It is strange. In my plays I never had such a problem (but I did not yet play with the new build) that I could not explain.
The only problems that disrupted my lines were
1) when I made some changes on the line, such as changing stations or rails, that interrupted it (and unfortunately train fever often cancels all output – even when changes are made in pause – and this is really a bug that they should consider fixing)
2) when the frequency of my trains dropped because the line got busier, because of more time loading/unloading goods or because trains were stuck due to signalling or electrification problems
The only other explanation I can think of is that the game (or you) built some new roads which made delivery “by foot” faster than your lines (but it is improbable that all seven cities display this problem at the same time).
If you can, it would be great if you send developers (or even here in the forum) the savegame just before that occurs… maybe with the savegame we could be able to tell what is going on.
