Right click on the title bar of any app launched via a docked app-icon. select attributes and go to the "application Specific" pull down. This gives some check boxes - checking "No Aplication Icon" will place three dots "..." on the docked app icon. These dots indicate that you can now launch multiple instances of this application via its icon. Upstream builds still work in this regard but this is somehow broken in Gentoo and has been for about 3 releases of windowmaker.