If the PATH on a Windows agent step is truncated after 1024 characters, Microsoft has provided a hotfix for this known Windows bug.
See Microsoft's problem description at:
The article title is: "A returned path environment variable is truncated to 1,024 bytes on a Windows Server 2003-based or Windows XP-based computer."
To get the hotfix, request it from Microsoft by clicking a link near the bottom of the page. Make sure to provide information about which operating system (XP, 2003) and Service Pack level you are using.
You can work around this problem temporarily by defining your PATH to fewer than 1024 characters and then adding other elements to it inside your script. The 1024 character limit is imposed at the point where the ElectricCommander Agent starts a process (that is, a step). After that, you should be able to add more characters to the PATH, up to the normal limit of 2048 characters.
Windows Server 2003 Service Pack 2 contains the hotfix http://support.microsoft.com/kb/914962/