First all.. thanks for adapting the whole game to newer windows and without CD, i bougth it even tought i allready owned the original game ^^
Game runs ok, i had to apply W98 compatibility to solve the mouse issue..
missions ran ok, but i got a problem.. during flight.. there are several transparency issues.. they seem to be related to black areas.. the frames of the cockpit windows are seen "nasty" against the space.. like if the blacks on the 2D art is transparent.. and some planets (earth for example) are half transparent.. also in the black zones of them , earth for example looks totally broken and can see througth her..
For the rest of the graphics, they seem to run ok.
any idea?

What video card / drivers do you have?
I'm sure I've seen that symptom before, years ago, but I forget which Glide wrapper I was using at the time. I would have had a GeForce4 Ti4200 at the time, and IIRC the available wrappers were less than ideal at the time.
You may wish to try out dgVoodoo for a possible fix (see thread here).

Im using a GF 7950GT , i will give it a look at the dgVoodo.. thanks!
Ok, i think it worked!
Now i dont see transparency where its not suposed..
Tought i had to try variations of the method (using the "closest to hardware" option made the game ghost like hell even within the menus ..
I ended using forced 32bit textures.. only problem is that when cutscenes play i see the lower part of the cockpit in the inferior black letter box margin under the cutscene