Although this problem also existed in RTB's server preferences, I am currently using Blockland Glass.
When I try to edit the preferences for mods I have loaded onto the server, not all the mods' preferences are shown. The mods are clearly enabled, as they are functioning properly, but the default settings get in the way of what I am trying to do with my server. Is there any reason the settings might not be showing? Come to think of it, only mods downloaded from the RTB archive seem to have their preferences displayed.
This problem has persisted for as long as I can remember, but I have found no mention of it happening to anyone else. Am I missing something?