While coding JSFL in the last few days, I found out from iterating through the library items that the items don't come in the order you see in the folder. They come in alphabetical order of the item name (sans the folder path).

Also, certain operations change the properties of an object. For example, by calling timeline.addNewLayer, you also change the property of the timeline.currentLayer to point to the newly inserted layer. The JSFI API documentation does a very poor job of explaining the side-effects for each function in the JSFL API. For example, it doesn't tell you when you should use setSelectedLayers, and how this call is related to currentLayer.