I created a new version ot the layer-combine-with-all-layers script.
This is a complete new script.
Although the menu looks nearly similar, it is as different as the complete script is.
The discription of the function is more logical and the actions give a logic output.
Remember to remove the old layer-combine-with-all-layers.scm from your scripts folder if you have already downloaded it.
The script works for GIMP 2.7+ and is tested in windows 7.
This is the final version of the script. If there are any problems with the script, if you like it or if you don't like it feel free to leave a comment.
(Update: I added a script to size all layers to the image and added the undo freeze for the new image to save memory.
The simple gif animations show one example of what is possible with this script Movie3.gif is the merged version with the green ball on top)
*I forgot to tell:
you can find the scripts under layers menu
Happy merging! :)