I just reset the target locations using ApUtilities>Additional Utilities>Reset Target Locations then choosing "All Applications". Then I checked the target locations using ApUtlities>Set Target Locations.
The raster space file path for ApUtilitiesConfig and DefaultConfig report an erorr when I simply opened them and tried to save them without changing. When I remove the path (For example the ApUtilitiesConfig Raster path is P:\ArcHydro\Zone_1\zone1_2013a.gdb and I change it to P:\ArcHydro\Zone_1\, it saves without an error).
Seems someone at ESRI should look into this...
BTW, the HydroConfig locations are set correctly.
