Testing on vanilla upstream (commit 790fe2e558d93572f87b7f4117a54d899903c5bf), shutdown always shows strange refcount counts:
05/15/12 06:41:10 ThreadRPCServer method=stop
05/15/12 06:41:10 Flush(false)
05/15/12 06:41:10 refcount=-1054439
05/15/12 06:41:10 addr.dat refcount=128
05/15/12 06:41:10 blkindex.dat refcount=1054286
05/15/12 06:41:10 wallet.dat refcount=22
05/15/12 06:41:10 StopNode()
05/15/12 06:41:10 ThreadOpenConnections exiting
05/15/12 06:41:10 ThreadSocketHandler exiting
05/15/12 06:41:10 ThreadMessageHandler exiting
05/15/12 06:41:10 Flush(true)
05/15/12 06:41:10 refcount=-1054440
05/15/12 06:41:10 addr.dat refcount=129
05/15/12 06:41:10 blkindex.dat refcount=1054286
05/15/12 06:41:10 wallet.dat refcount=22
05/15/12 06:41:10 Bitcoin exiting