If this item has been grayed out, it means the particular application you are trying to deploy does not require changes to your startup.cmd. Likewise, if this option is checked but you do not wish WiseMachine to make changes to your starup.cmd, you can uncheck this option. Note that this option affects only the startup.cmd. It has nothing to do with the system startup folder. That's determined by the desktop WPS object creation process.
Some applications require a reboot before the program can be used.
If that's the case, you will see a WPS object indicating that a reboot is required.