Thanks, that helped when I had the same problem. More information about how I fixed it:
summary: to fix, open your color scheme file and save it
First, I uninstalled ColorHighlighter, with “Package Control: Remove Package” in the Command Palette. But even after quitting and relaunching Sublime Text, my selection color was still wrong. So I went to my Settings – User file (‘Preferences.sublime-settings’) and looked at the chosen "color_scheme". I then opened that referenced file for editing. On my Mac, it was in the folder ‘~/Library/Application Support/Sublime Text 2/Packages/Color Scheme - Default’. The lineHighlight and selection values control the highlight color – but they were already at the correct value, though my highlight color was still wrong. The highlight color reverted to normal when I saved the color scheme file – that must have prompted Sublime Text to refresh its color theme.