Vista environement variables and registry - problems

Hi All,
I've found some problems with environement variables, especially
%windir% and %ProgramFiles%.
In registry in HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Run I
have a couple of entries beginning with %windir% or %ProgramFiles%.
I've found they will not start when system is going up!
After I've changed %windir% to C:\Windows and %ProgramFiles% to C:
\Program Files, everything is working fine.

from CMD.EXE, when I run SET I can see those variables.

What is wrong??

cheers,
Wojtek