This is an odd one! One thought and some questions in case the fix doesn’t help. My first inclination is something to do with Oomph. Oomph attempts to track and reapply preferences saved into a directory under User Home. This can cause fighting with styling preferences that our theme sets. While we have a fix in CI 9 to intercept and stop this fighting, for you, it may involve going to ~/.eclipse and removing folders that have oomph in the name. Be sure to delete/rename these after exiting Eclipse. When you next run, make sure that the preference recorder is not enabled at the bottom left of the Preferences page unless you really want to use Oomph.
Now, if Oomph isn’t the actual issue, could you provide some more details? Specifically two configuration files from your system:
Eclipse/configuration/.settings/com.genuitec.eclipse.theming.ui.prefs
(workspace)/.metadata/.plugins/org.eclipse.core.runtime/.settings/com.genuitec.eclipse.theming.ui.prefs
Thanks kindly!