The Make VB6 action looks for the default value under the following registry keys:
Code:
HKEY_CLASSES_ROOT\VisualBasic.Project\shell\Make\command
HKEY_CLASSES_ROOT\VisualBasic.Project\shell\open\command
and if found, strips off anything following .exe and uses that filename for the VB6 executable.
You may need to repair or reinstall VB6 if this isn't working.