G4StackingMessenger's destructor does not delete all of the objects that are created in the constructor. The one that is left out is verboseCmd. 

G4StackingMessenger::G4StackingMessenger(G4StackManager * fCont)
:fContainer(fCont)
{
  ...

  verboseCmd = new G4UIcmdWithAnInteger("/event/stack/verbose",this);
  
  ...

}

G4StackingMessenger::~G4StackingMessenger()
{
  delete statusCmd;
  delete clearCmd;
  delete stackDir;
  //need to add:
  //delete verboseCmd;
}

This causes the following memory leak (output from Valgrind)

==9625== 584 (108 direct, 476 indirect) bytes in 1 blocks are definitely lost in loss record 275 of 280
==9625==    at 0x402641D: operator new(unsigned int) (vg_replace_malloc.c:255)
==9625==    by 0x462171E: G4StackingMessenger::G4StackingMessenger(G4StackManager*) (G4StackingMessenger.cc:60)
==9625==    by 0x462073F: G4StackManager::G4StackManager() (G4StackManager.cc:43)
==9625==    by 0x45F3890: G4EventManager::G4EventManager() (G4EventManager.cc:64)
==9625==    by 0x45BFD71: G4RunManagerKernel::G4RunManagerKernel() (G4RunManagerKernel.cc:102)
==9625==    by 0x45B9E20: G4RunManager::G4RunManager() (G4RunManager.cc:85)

Adding the line:
delete verboseCmd;
to the destructor will fix this issue.