Hey Thorsten,
There is a Krakatoa log window, that you can open through the Preferences rollout in the Krakatoa GUI (There is also a handy macroscript for making a tollbar button that does this). I don’t think it currently gets errors that are out of pop-up windows though. I can definitely see the value in that so I’ll put it on my list of things TODO.
I’ll check out your BIN issue ASAP. It sounds like something that could happen, and a temporary work-around might be to save to a PRT file, then make a new PRT Loader with just that file, no culling, which then gets saved into a BIN file. That will avoid the -1 particles error.