Quick question, since I've been having this problem as well: My last debug.err is a whopping 118kb, and full of about 50,000 completely different types of errors, like...
 
Debug Message:  WARNING: Forest type  leaked - refs: 384
Debug Message:  WARNING: Forest type  leaked - refs: 99
Debug Message:  WARNING: GameItemType TravelingBoots leaked - refs: 19
Debug Message:  WARNING: GameItemType LongstriderBoots leaked - refs: 5
and...
 
Debug Message:  WARNING: Creating caravan Caravan at tile 72,35 with no city at that tile, no home city set
Debug Message:  WARNING: AI Player couldn't find a default difficulty level.
and...
 
Debug Message:  WARNING: (CXFileData) FindRegisteredMaterialIDByName could not find registered material with name 'lambert2SG'
Debug Message:  (WARNING) InitMaterialIDs could not find material ID for material 'lambert2SG'.  No attributes have been applied to this material in the modelling program.  Please add the material name attribute.
and...
 
Debug Message:  ERROR: (CD3D9Renderer) Unable to create mesh during ::CreateTextMesh.
Debug Message:  ERROR: (CDrawManager) Failed to create text mesh in ::Reload3DFont.
 
and...
Debug Message:  ERROR: (CMapTextGraphic) Failed to create 3D font wrapper for CMapTextGraphic 'The land of happy Youths'.
Debug Message:  WARNING: Could not find animation 'K_Wagon_Idle_01' in animation sub pack 'K_Wagon_Idle_Animations' for animation pack 'WagonAnimationPack'
Debug Message:  WARNING: Could not find animation 'K_Wagon_Walk_01' in animation sub pack 'K_Wagon_Walk_Animations' for animation pack 'WagonAnimationPack'
 
and...
Debug Message:  ERROR: (CD3D9Renderer) Failed to stretch a surface rect in ::StretchRect with error D3DERR_INVALIDCALL (Invalid call)
 
and...
 
Debug Message:  WARNING: Caravan Caravan has trade cities set, but for some reason has no directive!!  Continuing on to our next city to try to get on track again
Debug Message:  WARNING: Unit Aluembamo failed to start a new city, won't be consumed
 
and...
 
DebugMessage:  Unallocated Mem: 1404 bytes of memory from line 222 of E:\Elemental\Kumquat3D\Source\AStarManager.cpp
DebugMessage:  Unallocated Mem: 1404 bytes of memory from line 222 of E:\Elemental\Kumquat3D\Source\AStarManager.cpp
DebugMessage:  Unallocated Mem: 1404 bytes of memory from line 222 of E:\Elemental\Kumquat3D\Source\AStarManager.cpp
DebugMessage:  Not all memory has been freed from memory system AStar.
DebugMessage:     32292 bytes of memory still allocated.
 
This is all just a tiny sample.
....Is this because I'm playing in windowed mode or something?