Found the cause. For some mysterious reason, a registry entry was missing. When the registry entries were added, SCCM Console started working. The entries are,
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\ConfigMgr10\AdminUI\QueryProcessors\WQL]
"Assembly Path"="C:\\Program Files (x86)\\Microsoft Configuration Manager\\AdminConsole\\bin\\AdminUI.WqlQueryEngine.dll"
"Depends On"=""
"Type"="Microsoft.ConfigurationManagement.ManagementProvider.WqlQueryEngine.WqlConnectionManager"
No idea why these were not added, even after re-install.