When configuring a shortcut or running an executable from explorer, you have the option to run 16bit applications in a separate VDM (Virtual DOS Machine). If you always check run in separate memory space, you can make that the default behavior by editing the registry at:

HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/WOW

Edit or Add Value of type REG_SZ with value name DefaultSeparateVDM and set it to yes. The default behavior is no.

Reboot.