Are you using elements from a linked model by any chance? If so, then read my post here, as its the same problem, in which case, there will be a solution coming in BimorphNodes BoundingBox.GetElementsInside and BoundingBox.GetElementsIntersect which do the same thing as Tool.GetSurroundingElements
The other issue you may have is the tolerance input; I believe this node was developed before Dynamo adopted the active working units from Revit which meant units were always fixed. Hence, Tool.GetSurroundingElements tolerance inputs must be in Revit internal units to get consistent results (decimal feet). Alternatively, BimorphNodes BoundingBox nodes use whatever your active file units are, and will convert them dynamically to Revit internal units as its more intuitive.