I really wanted to use the player color cyan but It is not cyan ingame... Is there any way to fix this?

No.

But there are actually 255 colors maybe you find a color that is nearly cyan ingame.
Notice that some colors are different on different tilesets.
When using ScmDraft 2 just type the number in the field where you can choose the color.

Hahaha I like how you said it looks like vomit. I've always disliked the way it looked but vomit never crossed my mind.

What tileset?

Well don't know how to clarify that... O.o

Maybe you understand if I write it this way:
When you found a color on lets say jungle and want to use this color also on your other map using badlands it MAY BE that the color is different on the other map (due to different tileset). This is for the extended colors only ofc.

the cyan, darkgreen etc used to work in previous version i believe.... or maybe im just imagining things again.

Extended colours used to glow, now they just look like well, vomit. YOu're gonna have to experiment to find out what works, and you cant place any flags for players of extended colour.

Well, it really depends on the color, some just have some random unit portrait.