Descriptive Problem Summary:
Editing certain new variables through the map editor (step_x/y) will not properly save as a new "instance" of the object. It won't show up in the available instance list under the mini-map, nor will the values themselves properly save. If you right click > Make Active Object and place a duplicate of the object, the edited variable will be marked as edited with bold text, but it will be set to the original value. If you edit an additional value, like the object's name, then it will properly show up in the instance list, but the step_x/y (and possibly other vars?) still won't be loaded properly.
Numbered Steps to Reproduce Problem:
Place an object on the map
Right Click > Edit its step_y to 16
Right click > Make Active Object
Place another copy of the offset object
Right Click > Edit > notice step_y is bold, but set to 0