I’ve been having the same problem since upgrading to Oxygen. I haven’t been able to reliably reproduce the issue.
The workaround suggested by @howlger has helped and is less intrusive than blowing away the entire workspace:
- Close Eclipse.
- In the Eclipse workspace directory, delete the
.metadata\.plugins\org.eclipse.e4.workbench\workbench.xmi
file or just rename it so you can bring it back in case you need to revert. - Open Eclipse.
- Rearrange the UI elements to your liking.
This is a pain, but does remove the duplicate elements from toolbars.
I also found that customizing the perspective doesn’t work for duplicated items, but does for non-duplicated:
- Window -> Perspective -> Customize Perspective…
- On the “Tool Bar Visibility” tab, deselect the items that are cluttering up your toolbar.