I have the same problem with LT 2006. Clear reinstall and changes in registry was done, but it still doesn't appear.
I know that with LT 2006 you can change the window positions editing "Bounds" in HKEY_CURRENT_USER\Software\Autodesk\AutoCAD\R11\ACAD-4001:415\Profiles\
Dialogs\LayerManager
But here there's no even "LayerManager" key.
SP1 installed. System: Windows XP.
Have completly no idea what can it be...