Color configuration is not saved

[flg]

Eclipse 4.9 (but this problem has been here for as long as I can remember)
Linux 64 bits

In Glance Preferences, change the highlight color, Apply and Close. Works fine.
Restart Eclipse: colors are back to default settings.

As far as I can tell, the other settings are remembered properly.

[flg]

I found by accident that, upon Eclipse startup, the Eclipse Updater runs a startup tasks. There are some log messages there; one reads:
Performing Preference /instance/org.eclipse.ui.editors/glanceColorBackground = 255,128,0
And indeed after loading one can see that the config file (workspace/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.editors.prefs) contains the default value (255,128,0).

I went into the Oomph configuration (Oomph -> Setup Tasks -> Preference Recorder). There, in "user" records, the glanceColorBackground parameter was selected. Deselecting it fixed the issue.