Brian: The “Optimise for GIF” feature basically destroys a bunch of data which doesn’t change from one layer to the next, effectively creating a visual diff between successive layers to have as little as possible information in them, and still have the same animation.
The problem is that the operation destroys a bunch of user data, and this is one of those situations where we assume that the user knows what they’re doing. The GIF plug-in saves what you give it.
We could have an option in the GIF plug-in, have it on by default, and optimise the image as an export operation when someone saves a multi-layer image as GIF, I suppose. But if the user wants to keep all the info, we’re not going to tell him he can’t (we can also unoptimise animated GIFs, by the way). That would need a bugzilla number then…