I have a couple of ideas on how to fix this and I think it will actually be pretty easy, I'll have to do some testing though. I believe it's because 2.0 has an invisible inserter on the inside, and mine doesn't, but I could add it
edit: this will likely be one of the next things added in a future update, like within the next 2 days.
edit 2: I talked to some of the cybersyn devs, they might fix it on their end but I'm not too sure. a temporary solution is placing an inserter next to the rail as that's how cybersyn detects train configuration. alternatively, you can just set the train shape yourself with a combinator, completely bypassing cybersyn's inserter detection