Like, in the Riddle Room in DM you now need to place the correct object and then take it off to hear the clicking sound. Same thing a few levels later with the "lighter than feather"-puzzle. I know from experience that this is not intended behaviour

Look -> here <- for a simple example dungeon, if you don't want to go through the trouble of debugging DM or CSB dungeons. Just enter the teleporter, take the torch and the bread. The bread is supposed to be placed in the alcove to open the portcullis right next to it. (In this dungeon the alcove toggles the door, but same problem occurs with (de-)activation).
However, the same puzzle with 'constant weight' checked works out just the way it's supposed to.