Please note that this is not so much a bug but a side effect of way the modeler builds the runtime. This is not a new phenomenon: the debugger has never been available until the runtime has been fully started.
That means that a) this is not a minor fix but rather a major overhaul of the way the runtime is built and b) this would be considered a feature request rather than a bug. Your best bet at getting it implemented is gathering support in our idea forum, which Mendix uses to determine the most popular features to add to the roadmap.
If you need to debug it, temporarily take it off the configuration and stick it on a button. Then you can debug it.
We put plenty logging in the afterstartup mf so usually looking at the log will tell where it went wrong.