I have the same problem. SyncToy stops in the last subfolder and consumes 100% CPU. The log does not contain any information:
SYNC: 09/13/2009 10:35:09:406: -------------------------------------------------------------------------
SYNC: 09/13/2009 10:35:09:437: Starting SyncToy, version 2.0.100.0, built 12.08.2008 14:07:12.
SYNC: 09/13/2009 10:36:04:187: Started scanning directory : L:\Backups\Carsten\Arbeit\
SYNC: 09/13/2009 10:36:04:187: Started scanning directory : C:\Arbeit\
SYNC: 09/13/2009 10:36:12:109: Stopped scanning directory : C:\Arbeit\
SYNC: 09/13/2009 10:36:12:406: Stopped scanning directory : L:\Backups\Carsten\Arbeit\
SYNC: 09/13/2009 10:37:21:484: Started scanning directory : C:\Arbeit\
SYNC: 09/13/2009 10:37:21:484: Started scanning directory : L:\Backups\Carsten\Arbeit\
SYNC: 09/13/2009 10:37:31:312: Stopped scanning directory : C:\Arbeit\
SYNC: 09/13/2009 10:37:31:312: Stopped scanning directory : L:\Backups\Carsten\Arbeit\
SYNC: 09/13/2009 10:38:02:265: Started scanning directory : C:\Arbeit\
SYNC: 09/13/2009 10:38:02:265: Started scanning directory : L:\Backups\Carsten\Arbeit\
SYNC: 09/13/2009 10:38:09:968: Stopped scanning directory : L:\Backups\Carsten\Arbeit\
SYNC: 09/13/2009 10:38:10:187: Stopped scanning directory : C:\Arbeit\
It's a newly created folder pair. Deleting the subfolder does not help, Synctoy then stops in the new last subfolder.