This has been answered on the Eclipse Subversive forum here:
http://www.eclipse.org/forums/index.php/mv/msg/674039/1274614/#msg_1274614
To quote:
It is not the one of recommended layouts, so the automation is not available for it. In order to use such a layout you should open plug-in preferences and change the following option: Window->Preferences->Team->SVN->Project structure->Branch and Tag settings from "Respect project structure" to "Manual specification"
I have checked and it does seem to work, although unfortunately it is a global setting and not a per-project setting.