The colors are not inverting, it's actually because the game uses a color palette much like older games on the NES and SNES. The reason they are inverting, and most likely turning the pink white is because they do not match that palette. I am currently having the same issues.

You can find the palette in "Cortex Command\Base.rte" It's a BMP file. There is an old video about how to fix this issue by "converting" artwork to this palette.
https://www.youtube.com/watch?v=peMhNAntfTA

Sadly, it was made in 2007 and software used was Microsoft paint on XP OS.

There is a large forum about the "basics" of sprite making as well,

Main Forum post
http://forums.datarealms.com/viewtopic.php?f=1&t=16824

There is a sub-forum link called "How to Pixel: The Basics". I have looked around in there myself for the answer and found nothing.

another sub-forum is called "Problems with your mod's sprites?". It addresses the issue but actually doesn't do any more than the video. Seems like this is an outdated fix...

The around the last sub-forum is "How2Palette: Gimp Edition". This could possibly be a fix, but I personally have issues with GIMP on my computer so I am still stuck.

Hopefully you will or have already found a fix, if so... do tell. Good luck with future artwork.

Originally posted by NecroM:

The colors are not inverting, it's actually because the game uses a color palette much like older games on the NES and SNES. The reason they are inverting, and most likely turning the pink white is because they do not match that palette. I am currently having the same issues.

You can find the palette in "Cortex Command\Base.rte" It's a BMP file. There is an old video about how to fix this issue by "converting" artwork to this palette.
https://www.youtube.com/watch?v=peMhNAntfTA

Sadly, it was made in 2007 and software used was Microsoft paint on XP OS.

There is a large forum about the "basics" of sprite making as well,

Main Forum post
http://forums.datarealms.com/viewtopic.php?f=1&t=16824

There is a sub-forum link called "How to Pixel: The Basics". I have looked around in there myself for the answer and found nothing.

another sub-forum is called "Problems with your mod's sprites?". It addresses the issue but actually doesn't do any more than the video. Seems like this is an outdated fix...

The around the last sub-forum is "How2Palette: Gimp Edition". This could possibly be a fix, but I personally have issues with GIMP on my computer so I am still stuck.

Hopefully you will or have already found a fix, if so... do tell. Good luck with future artwork.

Oh sorry to mention but my new freind told me to use GraohicsGale and change the pallete to the CC pallete and now its fixed but thanks for the help though. :)

Thanks, I will have to try that... and you're welcome.

hmm, I have run into a problem. I don't have the Cortex Command Palette .pal file.

Did you find it online or create it custom or what?

Originally posted by NecroM:

hmm, I have run into a problem. I don't have the Cortex Command Palette .pal file.

Did you find it online or create it custom or what?

you can find the pallete in the steam guide "How to mod your first gun" and while reading it youll find a VERY small image of what looked like trails but its the pallete your looking for.