So I've painted a few liveries on the 77L and 77F and the paintkit always inserted one window on top of the fuselage just forward of the left side cargo door, nowhere else and in EVERY paint I tried to make. Since it was just one window it didn't bother me too much and I brushed it off.

 

But now I saw someone request a Swiss Air 77W repaint, and since it's incredibly easy I did it, but was met with an entire upper fuselage full of windows... and this was just ridiculous.

 

I'm probably doing something wrong, since there have been hundreds of liveries without these windows, but here was my process:

 

On the 77L and 77F it only put one window up top and I just dealt with it, but an entire line of windows is just ridiculous. But whats really odd is the left side has nothing!

 

I used the PMDG 77W paintkit, painted the Swiss stuff on the Fuse Master, cut each part to Fuse1, Fuse2 and Fuse3 then flipped it and saved as a .bmp, then used DXT Bitmap Manipulator to save it as a .dds DXT5

 

Here is the image with the windows:

 

https://farm6.staticflickr.com/5582/14863839672_c90202c089_o.png

You didn't flip the alpha, did you.