Normally, I have no problems when making custom plugins or editing existing ones. So if anyone would care to explain to me how this happened because I haven't got a clue. I just followed the same procedure as I normally do when making or editing plugins.
I didn't like having Voyager and her shuttles in a sublist as, by Federtion standards, it made no sense to have shuttle type vessels in a starship line-up when they should've been placed in the shuttle line-up. Moving the Delta Flyer 2, Type 8 and Type 9 shuttles didn't present me with this issue and they still work when launching them from Voyager. Just seems that the Aeroshuttle chose to 'not behave', lol.