Self-extracting Zip files created by WinZip Self-Extractor have 32-bit executable headers. As such, the self-extractors created by WinZip Self-Extractor run under the 64-bit Windows WOW64 subsystem which, as we understand it, provides a 32-bit environment including file system redirection. In particular, access attempts by 32-bit applications to the %windir%\system32 folder (containing 64-bit binaries) end up being redirected to the %windir%\SysWow64 folder (which contains the 32-bit binaries). Since the 64-bit CMD.EXE normally resides in the %windir%\system32 folder, we suspect that attempts to launch any .cmd file from 32-bit self-extractors end up being processed by the redirected, 32-bit %windir%\SysWow64\CMD.EXE instead.
You may also want to view the Best Practices for WOW64 document from Microsoft.