The EBE final structures can be tricky to snap.
I've found that grid snap mode doesn't work with the final object unless you placed the original EBE marker down while in grid snap mode, i'm assuming that the system creates the insertion point where you drop in the marker and if you don't do it in grid mode then it will be off set.
So basically:
1. Select to create a new EBE structure and hold it on the cursor over the editor screen (do not place it yet).
2. Press "B" twice to enter grid snapping mode.
3. Places the EBE structure marker and start editing.
4. When ready to move it into place exit EBE mode and select the EBE structure.
5. Select "extract" from the widget menu and move into position (it should already be in grid mode from before, but if you're moving it in a different session you may have to press "B" twice again to enter snapping mode).
(please note that the above may be old information, i haven't actually used the EBE since it was officially released, i only used it during the testing phase and this is the result i was getting, it may have been fixed since).
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