You can reset to the default color scheme in the Window>Preferences options page. This example will be for resetting a theme used for Java.
Navigate to Windows>Preferences>Java>Editor. Click on Syntax Coloring. Click “Restore Defaults” and “Apply“. Then, navigate to General>Editors. Click on Text Editors. Click on “Restore Defaults” and “Apply“.
I had the same issue and the above steps cleared up my problem. Also, the Show line numbers check box is on the last page from above.