When you do the print screen way of taking screenshots, it like takes a screenshot reversed of the image you had along with it being opositely mirrored. So i rotated all of the photo's to be correct, but i didn't want to go through the time of "inversing" the images 
Wait, what??
Mine show up normal, on multiple machines. So you're saying they're mirrored and rotated 180 degrees? Weird...
To me this sounds like some issue with S-99's image viewing program. Or rather not actual "issue" as in "bug", but some setting might be wrong... that could cause the program to use wrong starting point where it starts to open the image code.
The screenshots made by FS2_Open are RLE-coded TGA's. RLE (Run Length Encoding) can be done starting from different corners of picture. It's basically a line of pixel colour information; but instead of saying, for example, aaaaabbbbbbccdddd (if a, b, c and d were colours), it says a5b6c2d4 and so on... but the coding can be started from different corners of the actual image. If the picture is saved with RLE starting from one corner and image reading software thinks they are made starting from other corner, it ends up with screw-ups just like these, basically flipping/mirroring images without being told to do so.
GIMP shows FS2_Open screenshot TGA's just right. At least on my PC. What are you using, S-99?