I was misled by another problem.
My winexe is a 32 bits application which is running the 32 bits reg.exe on a 64 bits remote system (windows server 2003).
In this context, the key "HKEY_LOCAL_MACHINE\SOFTWARE" is silently pointing on the HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node Key of my remote system.
This is caused by the registry redirector of windows
http://msdn.microsoft.com/en-us/library/windows/desktop/aa384232%28v=vs.85%29.aspx
To avoid this redirection i had to force the use of the 64 bits reg.exe like this :
/usr/bin/winexe -U domain/login%"password" //host '**cmd /C %WINDIR%\sysnative\reg.exe** "QUERY" "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft Antimalware\Signature Updates"'