De meu blog
Bottom line, if your PATH environment variable is more than 2048 characters it (and WINDIR) stop being visible in many contexts.
I fixed it by manually running c:\windows\system32\systempropertiesadvanced.exe and deleting one entry from my PATH to put me under 2048 chars. New cmd windows work just fine.
Atualização: essa pergunta semelhante reivindicações 2047 é o máximo e elabora regras de expansão