Bobson

Same thing happens to me, although only with vessels without any kerbonaut space. As soon as there is at least one command pod (even unmanned) the problem is gone (at least for me). A useful workaround, but it'd rather not launch my probes from the top of empty command pod EDIT: Apparently, it was one of the mods - WernherChecker - that was causing it. As soon as I disabled it - no more problems. Hope it helps you too!