There are two "modes" for the frames: 1) combine where the fame is just put over whatever the image is, and replace where the current image is discarded and replaced by the frame. You can set these modes on each individual frame by adding (combine) or (replace) at the end of the frame name. You can also set this for all frames in the "Export as GIF" dialog.
It is also possible that Filters>Animations>Optimize (from GIF) does the right thing (in addition to optimizing the frames).
It is also possible that Filters>Animations>Optimize (from GIF) does the right thing (in addition to optimizing the frames).