Thanks for reading and for your question.
However, I don’t know Javalin and its behaviour. In your case, as you understand, the server is ready (serving port open and listening, therefore Cloud Run considers the server UP) before it has loaded all the routes to serve.
You should have boot option to prevent this situation. Maybe to perform eager loading instead of lazy loading. It’s a Javalin question more than a Cloud Run question.
However, in the alpha tester channel, I saw some message that talked about a readiness probe, to answer issues like yours. I don’t know if it’s in the roadmap.