Overlays Not retaining order?

[Momijisu]

I have several groups of overlay, the contents of which have a specific order, however when viewing the end product, both the groups and the layers inside those groups have reorganized

This only seems to affect some of the groups, one of the groups retained the correct order of layers inside, but still not in the right order of groups.

[Momijisu]

Further research seems to show that it ignores the order you put it into the layer groups, and bases the order on it's initialization order in the rest of the script?