Hey Glitch. Thats quite a story. Deffinetly gotta make sure of who or what for that matter your trying to pick up anywhere.

I thought that was a UFO when you posted the first shots. Now I see its an extremely cool UFO. (I could tell by the panel and the dome also I'm a little bit psychcic.)
Sounds like its the annimation and transparent poly glitch that I was talking about in one of the earlier posts. As far as I know there is no way to model it to keep the transparent polys and annimations in the same BGL. This I learned from Arno over at Scenerydesign.org. He knows just about everything when it comes to FS.
This is what I did to get around the problem when putting skylights in a hanger that has opening doors. As long as you do'nt need the transparent polys to move it should work.
In your Gmax scene select the transparent polys. Then click on your file drop down and click save selected. Save the polys as a seperate scene.
Then in FS find the exact Lat. Lon. you want for your main BGL.(Example N29* 52.52 W56* 25.45) by using the map function. You can place your main BGL with XML code so you can goup it with many other models to save space and file size. (I use Arnos OBplacer XML) Only thing is you can not place it with an FSUIPC plugin as you will have to use FS2002 gamepack Makemdl. to compile your transparent polys. If I remeber right XML wont let you place the two BGLs in the same place although you could try that with the transparent polys.
Now that you have saved your polys as a seperate scene in their original position in the BGL you can export them with FS2002 Makemdl. as BGL and on the scenery tab enter the exact Lat. Lon. as above and then place them in your scenery folder. This should put them exactly where they should be in the other BGL in FS. They may need to be in a seperate Scenery folder like this (UFO Glass scenery) or they may work in the same folder as the UFO scenery.
The only thing that may cause you a problem is as you rotate around the transparent polys in FS they may seem to appear and disapear. I do'nt know if this is the Sim trying to show how the glass looks at different angles or if it is part of a glitch that actualy makes them appear and disapear.
Rotating around here. You can see that I triggered the annimation to show you what it looks like. the annimation is not what is making them appear not to be there in this shot though.


This should work. But may not be satisfactory result in the end. This is the only way I know of to get around the problem. I have looked at many forums and posts and have not been able to find any other solutions. Let me know how things work out.
Good luck with your design.
(AN ODE TO GMAX) OOOOOOOOOOOHHHHHHHHH GMAX! How I sometimes want to hug and kiss it. And other times want to smash, berate, and delete it. Gmax how I love and loathe thee. The crashes the errors the reinstalls. Gmax you are the whomb of my a