To find the group number I want to animate, I use MeshWizard.

It's a basic and simple program, but I can't do without it...

Let's say you want to animate the airplane's propeller:
Press Info => Group Data
and there you have all the group numbers. (propeller is N# 14)

So yes, as Gattispilot said, the transparent "groups" (or elements) like a windshield must always be at the end of the list. (Otherwise, there's a transparency issue.)

And just one last thing: why vinka's Spacecraft ? You should use Fred18's Vesselbuilder instead.
The principle is the same, but it's compatible with Orbiter 2016 and 2024 and, above all, much more powerful...

I know this module very very well (a long time ago I even corresponded with Vinka and I think I'm the only one to have a beta version of Spacecraft 5...)
but honestly Fred18 has made an

module !!!