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They aren't specific to the version of Flash Builder. They are specific to your workspace. There is a .metadata folder outside of your workspace.
Within that navigate to .metadata\.plugins\org.eclipse.core.runtime\.settings
There are a bunch of .prefs files there. Try using those. I think what you might need is com.adobe.flexbuilder.editorcore.prefs.
Please do try and let me know if this works.
There are many files in there that affect the colour, I'm worried about corrupting the new workpace if I copy them in.
Try creating an entirely new workspace. Then test the colouring there. If it works out fine, you can import the project as an fxp from your old workspace to the new one. If it doesn't you can revert back to your old workspace.