I've tried poking around this forum for something like this but found nothing as well as I've tried this with both the latest 32 and 64 bit eduke32 builds and the problem still persists.
When selecting an item in the custom content box, EDuke32 loads the previous entry in that box, for example I will try to load "dukehard" but instead get the previous entry "duke64" loaded when I start EDuke32
