There is no mistake on your side. Leftmost tree has a custom-drawn scrollbar (I assume that's Draw2d tree) and rightmost tree shows native scrollbar (I guess those are the ones you call "JFace"). You can notice that most applications outside of Eclipse show scrollbars like the "JFace" ones. That is, if Ubuntu overlay scrollbars are enabled.
There is no easy fix for this. IMHO, you could try to get in Draw2d sources and try disabling their custom-drawn and replacing them with native ones (from SWT). Or you could use a custom tree instead on Nebula control...
Please note that "JFace" toolbars will look drastically different on Mac OS X or Windows, will have different size and such. And the users will expect them :)