Studio 2003 Pro + Platform SDK = no run

I’ve had Studio .Net ’03 Pro (MSDNAA service at school) for a whilebut I just recently installed the latest platform SDK (Server 2003 SP1) for use on XP Pro. Everything was fine until I “Registered PSDK Directories with Visual Studio”. The process seemed to delete all of my VC++ build directories (executable files, include, reference, library, and source) making it impossible to compile anything. I tracked down and restored the original paths and I can now build and compile win32 and MFC applications but it still will not compile any command line apps. Both STL and standard header files are not found even though the paths to the directories are correct and the files are located in the correct folders. I am stumped and have tried everything I can think of to correct the problem. Any help or suggestions Thanks.