Without more information I can only guess, but it's probably a 32- vs 64-bit difference.
http://www.kinook.com/VisBuildPro/Manual/6432bit.htm
Visual Build v7 is a 32-bit application, so to compare with running outside of Visual Build, you would need to run the 32-bit cmd.exe or wscript.exe/cscript.exe (in C:\Windows\SysWOW64).
If that doesn't help, please send the information requested at
http://www.kinook.com/Forum/showthread.php?t=3044.