ToME: the Tales of Maj'Eyal

I think this issue mainly pertains to Adventurers in the AoA campaign, since they spawn with both the Transmutation Chest and the Automated Portable Extractor. It seems that the APE takes precedence over the Trans Chest, so you never get Sher'Tul Fortress energy when transmuting items.

It would probably be best to just have the APE give energy when transmuting if the character has the fortress unlocked.

You can use one of the chests when nothing in is them to switch use over to that one. You choose to get either crafting mats or fortress energy this way.